always install them.
Examples and the demo have been updated to 3.0.
The double precision, small endian bug has been fixed.
--- /dev/null
+.TH do_dssp 1 "Tue 15 May 2001"
+.SH NAME
+do_dssp
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3do_dssp\fP
+.BI "-f" " traj.xtc "
+.BI "-s" " topol.tpr "
+.BI "-n" " index.ndx "
+.BI "-ssdump" " ssdump.dat "
+.BI "-map" " ss.map "
+.BI "-o" " ss.xpm "
+.BI "-sc" " scount.xvg "
+.BI "-a" " area.xpm "
+.BI "-ta" " totarea.xvg "
+.BI "-aa" " averarea.xvg "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-[no]w" ""
+.BI "-sss" " string "
+.SH DESCRIPTION
+do_dssp
+reads a trajectory file and computes the secondary structure for
+each time frame
+calling the dssp program. If you do not have the dssp program,
+get it. do_dssp assumes that the dssp executable is in
+/home/mdgroup/dssp/dssp. If that is not the case, then you should
+set an environment variable
+.B DSSP
+pointing to the dssp
+executable as in:
+
+
+
+.B setenv DSSP /usr/local/bin/dssp
+
+
+
+The structure assignment for each residue and time is written to an
+
+.B .xpm
+matrix file. This file can be visualized with for instance
+
+.B xv
+and can be converted to postscript with
+.B xpm2ps
+.
+The number of residues with each secondary structure type and the
+total secondary structure (
+.B -sss
+) count as a function of
+time are also written to file (
+.B -sc
+).
+
+
+Solvent accessible surface (SAS) per residue can be calculated, both in
+absolute values (A2) and in fractions of the maximal accessible
+surface of a residue. The maximal accessible surface is defined as
+the accessible surface of a residue in a chain of glycines.
+[B]Note[b] that the program
+.B g_sas
+can also compute SAS
+and that is more efficient.
+
+
+Finally, this program can dump the secondary structure in a special file
+
+.B ssdump.dat
+for usage in the program
+.B g_chi
+. Together
+these two programs can be used to analyze dihedral properties as a
+function of secondary structure type.
+.SH FILES
+.BI "-f" " traj.xtc"
+.B Input
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-s" " topol.tpr"
+.B Input
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
+
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
+.BI "-ssdump" " ssdump.dat"
+.B Output, Opt.
+ Generic data file
+
+.BI "-map" " ss.map"
+.B Input, Lib.
+ File that maps matrix data to colors
+
+.BI "-o" " ss.xpm"
+.B Output
+ X PixMap compatible matrix file
+
+.BI "-sc" " scount.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-a" " area.xpm"
+.B Output, Opt.
+ X PixMap compatible matrix file
+
+.BI "-ta" " totarea.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-aa" " averarea.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " -1"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " -1"
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " -1"
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-[no]w" " no"
+ View output xvg, xpm, eps and pdb files
+
+.BI "-sss" " string" " HEBT"
+ Secondary structures for structure count
+
+.SH DIAGNOSTICS
+\- The program is very slow
+
--- /dev/null
+.TH editconf 1 "Tue 15 May 2001"
+.SH NAME
+editconf
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3editconf\fP
+.BI "-f" " conf.gro "
+.BI "-n" " index.ndx "
+.BI "-o" " out.gro "
+.BI "-bf" " bfact.dat "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-[no]w" ""
+.BI "-[no]ndef" ""
+.BI "-bt" " enum "
+.BI "-box" " vector "
+.BI "-angles" " vector "
+.BI "-d" " real "
+.BI "-[no]c" ""
+.BI "-center" " vector "
+.BI "-rotate" " vector "
+.BI "-[no]princ" ""
+.BI "-scale" " vector "
+.BI "-density" " real "
+.BI "-[no]pbc" ""
+.BI "-[no]mead" ""
+.BI "-[no]grasp" ""
+.BI "-rvdw" " real "
+.BI "-[no]atom" ""
+.BI "-[no]legend" ""
+.BI "-label" " string "
+.SH DESCRIPTION
+editconf converts generic structure format to
+.B .gro
+,
+.B .g96
+
+or
+.B .pdb
+.
+
+
+
+The box can be modified with options
+.B -box
+,
+.B -d
+and
+
+.B -angles
+. Both
+.B -box
+and
+.B -d
+
+will center the system in the box.
+
+
+
+Option
+.B -bt
+determines the box type:
+.B tric
+is a
+triclinic box,
+.B cubic
+is a cubic box,
+.B dodecahedron
+is
+a rhombic dodecahedron and
+.B octahedron
+is a truncated octahedron.
+The last two are special cases of a triclinic box.
+The length of the three box vectors of the truncated octahedron is the
+shortest distance between two opposite hexagons.
+The volume of a dodecahedron is 0.71 and that of a truncated octahedron
+is 0.77 of that of a cubic box with the same periodic image distance.
+
+
+
+Option
+.B -box
+requires only
+one value for a cubic box, dodecahedron and a truncated octahedron.
+With
+.B -d
+and
+.B tric
+the size of the system in the x, y
+and z directions is used. With
+.B -d
+and
+.B cubic
+,
+
+.B dodecahedron
+or
+.B octahedron
+the diameter of the system
+is used, which is the largest distance between two atoms.
+
+
+
+Option
+.B -angles
+is only meaningful with option
+.B -box
+and
+a triclinic box and can not be used with option
+.B -d
+.
+
+
+
+When
+.B -n
+or
+.B -ndef
+is set, a group
+can be selected for calculating the size and the geometric center,
+otherwise the whole system is used.
+
+
+
+
+.B -rotate
+rotates the coordinates and velocities.
+
+.B -princ
+aligns the principal axes of the system along the
+coordinate axes, this may allow you to decrease the box volume,
+but beware that molecules can rotate significantly in a nanosecond.
+
+
+Scaling is applied before any of the other operations are
+performed. Boxes can be scaled to give a certain density (option
+
+.B -density
+). A special feature of the scaling option, when the
+factor -1 is given in one dimension, one obtains a mirror image,
+mirrored in one of the plains, when one uses -1 in three dimensions
+a point-mirror image is obtained.
+
+
+Groups are selected after all operations have been applied.
+
+
+Periodicity can be removed in a crude manner.
+It is important that the box sizes at the bottom of your input file
+are correct when the periodicity is to be removed.
+
+
+
+The program can optionally rotate the solute molecule to align the
+molecule along its principal axes (
+.B -rotate
+)
+
+
+
+When writing
+.B .pdb
+files, B-factors can be
+added with the
+.B -bf
+option. B-factors are read
+from a file with with following format: first line states number of
+entries in the file, next lines state an index
+followed by a B-factor. The B-factors will be attached per residue
+unless an index is larger than the number of residues or unless the
+
+.B -atom
+option is set. Obviously, any type of numeric data can
+be added instead of B-factors.
+.B -legend
+will produce
+a row of CA atoms with B-factors ranging from the minimum to the
+maximum value found, effectively making a legend for viewing.
+
+
+
+With the option -mead a special pdb file for the MEAD electrostatics
+program (Poisson-Boltzmann solver) can be made. A further prerequisite
+is that the input file is a run input file.
+The B-factor field is then filled with the Van der Waals radius
+of the atoms while the occupancy field will hold the charge.
+
+
+
+The option -grasp is similar, but it puts the charges in the B-factor
+and the radius in the occupancy.
+
+
+
+Finally with option
+.B -label
+editconf can add a chain identifier
+to a pdb file, which can be useful for analysis with e.g. rasmol.
+.SH FILES
+.BI "-f" " conf.gro"
+.B Input
+ Generic structure: gro g96 pdb tpr tpb tpa
+
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
+.BI "-o" " out.gro"
+.B Output
+ Generic structure: gro g96 pdb
+
+.BI "-bf" " bfact.dat"
+.B Input, Opt.
+ Generic data file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 0"
+ Set the nicelevel
+
+.BI "-[no]w" " no"
+ View output xvg, xpm, eps and pdb files
+
+.BI "-[no]ndef" " no"
+ Choose output from default index groups
+
+.BI "-bt" " enum" " tric"
+ Box type for -box and -d: tric, cubic, dodecahedron or octahedron
+
+.BI "-box" " vector" " 0 0 0"
+ Box vector lengths (a,b,c)
+
+.BI "-angles" " vector" " 90 90 90"
+ Angles between the box vectors (bc,ac,ab)
+
+.BI "-d" " real" " 0"
+ Distance between the solute and the box
+
+.BI "-[no]c" " no"
+ Center molecule in box (implied by -box and -d)
+
+.BI "-center" " vector" " 0 0 0"
+ Coordinates of geometrical center
+
+.BI "-rotate" " vector" " 0 0 0"
+ Rotation around the X, Y and Z axes in degrees
+
+.BI "-[no]princ" " no"
+ Orient molecule(s) along their principal axes
+
+.BI "-scale" " vector" " 1 1 1"
+ Scaling factor
+
+.BI "-density" " real" " 1000"
+ Density (g/l) of the output box achieved by scaling
+
+.BI "-[no]pbc" " no"
+ Remove the periodicity (make molecule whole again)
+
+.BI "-[no]mead" " no"
+ Store the charge of the atom in the occupancy field and the radius of the atom in the B-factor field
+
+.BI "-[no]grasp" " no"
+ Store the charge of the atom in the B-factor field and the radius of the atom in the occupancy field
+
+.BI "-rvdw" " real" " 0.12"
+ Default Van der Waals radius if one can not be found in the database
+
+.BI "-[no]atom" " no"
+ Force B-factor attachment per atom
+
+.BI "-[no]legend" " no"
+ Make B-factor legend
+
+.BI "-label" " string" " A"
+ Add chain label for all residues
+
+.SH DIAGNOSTICS
+\- For complex molecules, the periodicity removal routine may break down, in that case you can use trjconv
+
--- /dev/null
+.TH eneconv 1 "Tue 15 May 2001"
+.SH NAME
+eneconv
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3eneconv\fP
+.BI "-f" " ener.edr "
+.BI "-o" " fixed.edr "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-b" " real "
+.BI "-e" " real "
+.BI "-dt" " real "
+.BI "-offset" " real "
+.BI "-[no]settime" ""
+.BI "-[no]sort" ""
+.BI "-scalefac" " real "
+.BI "-[no]error" ""
+.SH DESCRIPTION
+When
+.B -f
+is
+.I not
+specified:
+
+Concatenates several energy files in sorted order.
+In case of double time frames the one
+in the later file is used. By specifying
+.B -settime
+you will be
+asked for the start time of each file. The input files are taken
+from the command line,
+such that the command
+.B eneconv -o fixed.edr *.edr
+should do
+the trick.
+
+
+With
+.B -f
+specified:
+
+Reads one energy file and writes another, applying the
+.B -dt
+,
+
+.B -offset
+,
+.B -t0
+and
+.B -settime
+options and
+converting to a different format if necessary (indicated by file
+extentions).
+
+
+
+.B -settime
+is applied first, then
+.B -dt
+/
+.B -offset
+
+followed by
+.B -b
+and
+.B -e
+to select which frames to write.
+.SH FILES
+.BI "-f" " ener.edr"
+.B Input
+ Generic energy: edr ene
+
+.BI "-o" " fixed.edr"
+.B Output, Opt.
+ Generic energy: edr ene
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " real" " -1"
+ First time to use
+
+.BI "-e" " real" " -1"
+ Last time to use
+
+.BI "-dt" " real" " 0"
+ Only write out frame when t MOD dt = offset
+
+.BI "-offset" " real" " 0"
+ Time offset for -dt option
+
+.BI "-[no]settime" " no"
+ Change starting time interactively
+
+.BI "-[no]sort" " yes"
+ Sort energy files (not frames)
+
+.BI "-scalefac" " real" " 1"
+ Multiply energy component by this factor
+
+.BI "-[no]error" " yes"
+ Stop on errors in the file
+
+.SH DIAGNOSTICS
+\- When combining trajectories the sigma and E2 (necessary for statistics) are not updated correctly. Only the actual energy is correct. One thus has to compute statistics in another way.
+
--- /dev/null
+.TH g_anaeig 1 "Tue 15 May 2001"
+.SH NAME
+g_anaeig
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3g_anaeig\fP
+.BI "-v" " eigenvec.trr "
+.BI "-v2" " eigenvec2.trr "
+.BI "-f" " traj.xtc "
+.BI "-s" " topol.tpr "
+.BI "-n" " index.ndx "
+.BI "-eig1" " eigenval1.xvg "
+.BI "-eig2" " eigenval2.xvg "
+.BI "-disp" " eigdisp.xvg "
+.BI "-proj" " proj.xvg "
+.BI "-2d" " 2dproj.xvg "
+.BI "-3d" " 3dproj.pdb "
+.BI "-filt" " filtered.xtc "
+.BI "-extr" " extreme.pdb "
+.BI "-over" " overlap.xvg "
+.BI "-inpr" " inprod.xpm "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-tu" " enum "
+.BI "-[no]w" ""
+.BI "-first" " int "
+.BI "-last" " int "
+.BI "-skip" " int "
+.BI "-max" " real "
+.BI "-nframes" " int "
+.BI "-[no]split" ""
+.SH DESCRIPTION
+
+.B g_anaeig
+analyzes eigenvectors. The eigenvectors can be of a
+covariance matrix (
+.B g_covar
+) or of a Normal Modes anaysis
+(
+.B g_nmeig
+).
+
+
+When a trajectory is projected on eigenvectors, all structures are
+fitted to the structure in the eigenvector file, if present, otherwise
+to the structure in the structure file. When no run input file is
+supplied, periodicity will not be taken into account. Most analyses
+are performed on eigenvectors
+.B -first
+to
+.B -last
+, but when
+
+.B -first
+is set to -1 you will be prompted for a selection.
+
+
+
+.B -disp
+: plot all atom displacements of eigenvectors
+
+.B -first
+to
+.B -last
+.
+
+
+
+.B -proj
+: calculate projections of a trajectory on eigenvectors
+
+.B -first
+to
+.B -last
+.
+The projections of a trajectory on the eigenvectors of its
+covariance matrix are called principal components (pc's).
+It is often useful to check the cosine content the pc's,
+since the pc's of random diffusion are cosines with the number
+of periods equal to half the pc index.
+The cosine content of the pc's can be calculated with the program
+
+.B g_analyze
+.
+
+
+
+.B -2d
+: calculate a 2d projection of a trajectory on eigenvectors
+
+.B -first
+and
+.B -last
+.
+
+
+
+.B -3d
+: calculate a 3d projection of a trajectory on the first
+three selected eigenvectors.
+
+
+
+.B -filt
+: filter the trajectory to show only the motion along
+eigenvectors
+.B -first
+to
+.B -last
+.
+
+
+
+.B -extr
+: calculate the two extreme projections along a trajectory
+on the average structure and interpolate
+.B -nframes
+frames
+between them, or set your own extremes with
+.B -max
+. The
+eigenvector
+.B -first
+will be written unless
+.B -first
+and
+
+.B -last
+have been set explicitly, in which case all eigenvectors
+will be written to separate files. Chain identifiers will be added
+when writing a
+.B .pdb
+file with two or three structures (you
+can use
+.B rasmol -nmrpdb
+to view such a pdb file).
+
+
+ Overlap calculations between covariance analysis:
+
+ NOTE: the analysis should use the same fitting structure
+
+
+
+.B -over
+: calculate the subspace overlap of the eigenvectors in
+file
+.B -v2
+with eigenvectors
+.B -first
+to
+.B -last
+
+in file
+.B -v
+.
+
+
+
+.B -inpr
+: calculate a matrix of inner-products between
+eigenvectors in files
+.B -v
+and
+.B -v2
+. All eigenvectors
+of both files will be used unless
+.B -first
+and
+.B -last
+
+have been set explicitly.
+
+
+When
+.B -v
+,
+.B -eig1
+,
+.B -v2
+and
+.B -eig2
+are given,
+a single number for the overlap between the covariance matrices is
+generated. The formulas are:
+
+ difference = sqrt(tr((sqrt(M1) - sqrt(M2))2))
+
+normalized overlap = 1 - difference/sqrt(tr(M1) + tr(M2))
+
+ shape overlap = 1 - sqrt(tr((sqrt(M1/tr(M1)) - sqrt(M2/tr(M2)))2))
+
+where M1 and M2 are the two covariance matrices and tr is the trace
+of a matrix. The numbers are proportional to the overlap of the square
+root of the fluctuations. The normalized overlap is the most useful
+number, it is 1 for identical matrices and 0 when the sampled
+subspaces are orthogonal.
+.SH FILES
+.BI "-v" " eigenvec.trr"
+.B Input
+ Full precision trajectory: trr trj
+
+.BI "-v2" " eigenvec2.trr"
+.B Input, Opt.
+ Full precision trajectory: trr trj
+
+.BI "-f" " traj.xtc"
+.B Input, Opt.
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-s" " topol.tpr"
+.B Input, Opt.
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
+
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
+.BI "-eig1" " eigenval1.xvg"
+.B Input, Opt.
+ xvgr/xmgr file
+
+.BI "-eig2" " eigenval2.xvg"
+.B Input, Opt.
+ xvgr/xmgr file
+
+.BI "-disp" " eigdisp.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-proj" " proj.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-2d" " 2dproj.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-3d" " 3dproj.pdb"
+.B Output, Opt.
+ Generic structure: gro g96 pdb
+
+.BI "-filt" " filtered.xtc"
+.B Output, Opt.
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-extr" " extreme.pdb"
+.B Output, Opt.
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-over" " overlap.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-inpr" " inprod.xpm"
+.B Output, Opt.
+ X PixMap compatible matrix file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " -1"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " -1"
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " -1"
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-tu" " enum" " ps"
+ Time unit: ps, fs, ns, us, ms, s, m or h
+
+.BI "-[no]w" " no"
+ View output xvg, xpm, eps and pdb files
+
+.BI "-first" " int" " 1"
+ First eigenvector for analysis (-1 is select)
+
+.BI "-last" " int" " 8"
+ Last eigenvector for analysis (-1 is till the last)
+
+.BI "-skip" " int" " 1"
+ Only analyse every nr-th frame
+
+.BI "-max" " real" " 0"
+ Maximum for projection of the eigenvector on the average structure, max=0 gives the extremes
+
+.BI "-nframes" " int" " 2"
+ Number of frames for the extremes output
+
+.BI "-[no]split" " no"
+ Split eigenvector projections where time is zero
+
--- /dev/null
+.TH g_analyze 1 "Tue 15 May 2001"
+.SH NAME
+g_analyze
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3g_analyze\fP
+.BI "-f" " graph.xvg "
+.BI "-ac" " autocorr.xvg "
+.BI "-msd" " msd.xvg "
+.BI "-cc" " coscont.xvg "
+.BI "-dist" " distr.xvg "
+.BI "-av" " average.xvg "
+.BI "-ee" " errest.xvg "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-[no]w" ""
+.BI "-[no]time" ""
+.BI "-b" " real "
+.BI "-e" " real "
+.BI "-n" " int "
+.BI "-[no]d" ""
+.BI "-bw" " real "
+.BI "-errbar" " enum "
+.BI "-[no]power" ""
+.BI "-[no]subav" ""
+.BI "-[no]oneacf" ""
+.BI "-acflen" " int "
+.BI "-[no]normalize" ""
+.BI "-P" " enum "
+.BI "-fitfn" " enum "
+.BI "-ncskip" " int "
+.BI "-beginfit" " real "
+.BI "-endfit" " real "
+.SH DESCRIPTION
+g_analyze reads an ascii file and analyzes data sets.
+A line in the input file may start with a time
+(see option
+.B -time
+) and any number of y values may follow.
+Multiple sets can also be
+read when they are seperated by & (option
+.B -n
+),
+in this case only one y value is read from each line.
+All lines starting with and @ are skipped.
+All analyses can also be done for the derivative of a set
+(option
+.B -d
+).
+
+
+All options, except for
+.B -av
+and
+.B -power
+assume that the
+points are equidistant in time.
+
+
+g_analyze always shows the average and standard deviation of each
+set. For each set it also shows the relative deviation of the third
+and forth cumulant from those of a Gaussian distribution with the same
+standard deviation.
+
+
+Option
+.B -ac
+produces the autocorrelation function(s).
+
+
+Option
+.B -cc
+plots the resemblance of set i with a cosine of
+i/2 periods. The formula is:
+2 (int0-T y(t) cos(pi t/i) dt)2 / int0-T y(t) y(t) dt
+
+This is useful for principal components obtained from covariance
+analysis, since the principal components of random diffusion are
+pure cosines.
+
+
+Option
+.B -msd
+produces the mean square displacement(s).
+
+
+Option
+.B -dist
+produces distribution plot(s).
+
+
+Option
+.B -av
+produces the average over the sets.
+Error bars can be added with the option
+.B -errbar
+.
+The errorbars can represent the standard deviation, the error
+(assuming the points are independent) or the interval containing
+90% of the points, by discarding 5% of the points at the top and
+the bottom.
+
+
+Option
+.B -ee
+produces error estimates using block averaging.
+A set is divided in a number of blocks and averages are calculated for
+each block. The error for the total average is calculated from
+the variance between averages of the m blocks B_i as follows:
+error2 = Sum (B_i - B)2 / (m*(m-1)).
+These errors are plotted as a function of the block size.
+Also an analytical block average curve is plotted, assuming
+that the autocorrelation is a sum of two exponentials.
+The analytical curve for the block average BA is:
+
+BA(t) = sigma sqrt(2/T ( a (tau1 ((exp(-t/tau1) - 1) tau1/t + 1)) +
+
+ (1-a) (tau2 ((exp(-t/tau2) - 1) tau2/t + 1)))),
+where T is the total time.
+a, tau1 and tau2 are obtained by fitting BA(t) to the calculated block
+average.
+When the actual block average is very close to the analytical curve,
+the error is sigma*sqrt(2/T (a tau1 + (1-a) tau2)).
+
+
+Option
+.B -power
+fits the data to b ta, which is accomplished
+by fitting to a t + b on log-log scale. All points after the first
+zero or negative value are ignored.
+.SH FILES
+.BI "-f" " graph.xvg"
+.B Input
+ xvgr/xmgr file
+
+.BI "-ac" " autocorr.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-msd" " msd.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-cc" " coscont.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-dist" " distr.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-av" " average.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-ee" " errest.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-[no]w" " no"
+ View output xvg, xpm, eps and pdb files
+
+.BI "-[no]time" " yes"
+ Expect a time in the input
+
+.BI "-b" " real" " -1"
+ First time to read from set
+
+.BI "-e" " real" " -1"
+ Last time to read from set
+
+.BI "-n" " int" " 1"
+ Read sets seperated by &
+
+.BI "-[no]d" " no"
+ Use the derivative
+
+.BI "-bw" " real" " 0.1"
+ Binwidth for the distribution
+
+.BI "-errbar" " enum" " none"
+ Error bars for -av: none, stddev, error or 90
+
+.BI "-[no]power" " no"
+ Fit data to: b ta
+
+.BI "-[no]subav" " yes"
+ Subtract the average before autocorrelating
+
+.BI "-[no]oneacf" " no"
+ Calculate one ACF over all sets
+
+.BI "-acflen" " int" " -1"
+ Length of the ACF, default is half the number of frames
+
+.BI "-[no]normalize" " yes"
+ Normalize ACF
+
+.BI "-P" " enum" " 0"
+ Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or 3
+
+.BI "-fitfn" " enum" " none"
+ Fit function: none, exp, aexp, exp_exp or vac
+
+.BI "-ncskip" " int" " 0"
+ Skip N points in the output file of correlation functions
+
+.BI "-beginfit" " real" " 0"
+ Time where to begin the exponential fit of the correlation function
+
+.BI "-endfit" " real" " -1"
+ Time where to end the exponential fit of the correlation function, -1 is till the end
+
--- /dev/null
+.TH g_angle 1 "Tue 15 May 2001"
+.SH NAME
+g_angle
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3g_angle\fP
+.BI "-f" " traj.xtc "
+.BI "-s" " topol.tpr "
+.BI "-n" " angle.ndx "
+.BI "-od" " angdist.xvg "
+.BI "-ov" " angaver.xvg "
+.BI "-of" " dihfrac.xvg "
+.BI "-ot" " dihtrans.xvg "
+.BI "-oh" " trhisto.xvg "
+.BI "-oc" " dihcorr.xvg "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-[no]w" ""
+.BI "-type" " enum "
+.BI "-[no]all" ""
+.BI "-binwidth" " real "
+.BI "-[no]chandler" ""
+.BI "-[no]avercorr" ""
+.BI "-acflen" " int "
+.BI "-[no]normalize" ""
+.BI "-P" " enum "
+.BI "-fitfn" " enum "
+.BI "-ncskip" " int "
+.BI "-beginfit" " real "
+.BI "-endfit" " real "
+.SH DESCRIPTION
+g_angle computes the angle distribution for a number of angles
+or dihedrals. This way you can check whether your simulation
+is correct. With option -ov you can plot the average angle of
+a group of angles as a function of time. With the -all option
+the first graph is the average, the rest are the individual angles.
+
+
+With the -of option g_angle also calculates the fraction of trans
+dihedrals (only for dihedrals) as function of time, but this is
+probably only fun for a selected few.
+
+
+With option -oc a dihedral correlation function is calculated.
+
+
+It should be noted that the indexfile should contain
+atom-triples for angles or atom-quadruplets for dihedrals.
+If this is not the case, the program will crash.
+.SH FILES
+.BI "-f" " traj.xtc"
+.B Input
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-s" " topol.tpr"
+.B Input
+ Generic run input: tpr tpb tpa
+
+.BI "-n" " angle.ndx"
+.B Input
+ Index file
+
+.BI "-od" " angdist.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-ov" " angaver.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-of" " dihfrac.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-ot" " dihtrans.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-oh" " trhisto.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-oc" " dihcorr.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " -1"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " -1"
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " -1"
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-[no]w" " no"
+ View output xvg, xpm, eps and pdb files
+
+.BI "-type" " enum" " angle"
+ Type of angle to analyse: angle, dihedral, improper or ryckaert-bellemans
+
+.BI "-[no]all" " no"
+ Plot all angles separately in the averages file, in the order of appearance in the index file.
+
+.BI "-binwidth" " real" " 1"
+ binwidth (degrees) for calculating the distribution
+
+.BI "-[no]chandler" " no"
+ Use Chandler correlation function (N[trans] = 1, N[gauche] = 0) rather than cosine correlation function. Trans is defined as phi -60 || phi 60.
+
+.BI "-[no]avercorr" " no"
+ Average the correlation functions for the individual angles/dihedrals
+
+.BI "-acflen" " int" " -1"
+ Length of the ACF, default is half the number of frames
+
+.BI "-[no]normalize" " yes"
+ Normalize ACF
+
+.BI "-P" " enum" " 0"
+ Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or 3
+
+.BI "-fitfn" " enum" " none"
+ Fit function: none, exp, aexp, exp_exp or vac
+
+.BI "-ncskip" " int" " 0"
+ Skip N points in the output file of correlation functions
+
+.BI "-beginfit" " real" " 0"
+ Time where to begin the exponential fit of the correlation function
+
+.BI "-endfit" " real" " -1"
+ Time where to end the exponential fit of the correlation function, -1 is till the end
+
+.SH DIAGNOSTICS
+\- Counting transitions only works for dihedrals with multiplicity 3
+
--- /dev/null
+.TH g_bond 1 "Tue 15 May 2001"
+.SH NAME
+g_bond
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3g_bond\fP
+.BI "-f" " traj.xtc "
+.BI "-n" " index.ndx "
+.BI "-o" " bonds.xvg "
+.BI "-l" " bonds.log "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-[no]w" ""
+.BI "-blen" " real "
+.BI "-tol" " real "
+.BI "-[no]aver" ""
+.SH DESCRIPTION
+g_bond makes a distribution of bond lengths. If all is well a
+gaussian distribution should be made when using a harmonic potential.
+bonds are read from a single group in the index file in order i1-j1
+i2-j2 thru in-jn.
+
+
+
+.B -tol
+gives the half-width of the distribution as a fraction
+of the bondlength (
+.B -blen
+). That means, for a bond of 0.2
+a tol of 0.1 gives a distribution from 0.18 to 0.22
+.SH FILES
+.BI "-f" " traj.xtc"
+.B Input
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-n" " index.ndx"
+.B Input
+ Index file
+
+.BI "-o" " bonds.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-l" " bonds.log"
+.B Output, Opt.
+ Log file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " -1"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " -1"
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " -1"
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-[no]w" " no"
+ View output xvg, xpm, eps and pdb files
+
+.BI "-blen" " real" " -1"
+ Bond length. By default length of first bond
+
+.BI "-tol" " real" " 0.1"
+ Half width of distribution as fraction of blen
+
+.BI "-[no]aver" " yes"
+ Sum up distributions
+
+.SH DIAGNOSTICS
+\- It should be possible to get bond information from the topology.
+
--- /dev/null
+.TH g_bundle 1 "Tue 15 May 2001"
+.SH NAME
+g_bundle
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3g_bundle\fP
+.BI "-f" " traj.xtc "
+.BI "-s" " topol.tpr "
+.BI "-n" " index.ndx "
+.BI "-ol" " bun_len.xvg "
+.BI "-od" " bun_dist.xvg "
+.BI "-ot" " bun_tilt.xvg "
+.BI "-otr" " bun_tiltr.xvg "
+.BI "-otl" " bun_tiltl.xvg "
+.BI "-oa" " axes.pdb "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-na" " int "
+.BI "-[no]z" ""
+.SH DESCRIPTION
+g_bundle analyzes bundles of axes. The axes can be for instance
+helix axes. The program reads two index groups and divides both
+of them in
+.B -na
+parts. The groups define the tops and
+bottoms of the axes. Several quantities are written to file:
+the axis length, the distance from the axis centers to the average
+center of all axes, the total tilt, the radial tilt and the lateral
+tilt with respect to the average axis.
+
+
+
+With option
+.B -oa
+the top, mid and bottom points of each axis
+are written to a pdb file each frame. The residue numbers correspond
+to the axis numbers. When viewing this file with
+.B rasmol
+use the
+command line option
+.B -nmrpdb
+, and type
+.B set axis true
+to
+display the reference axis.
+.SH FILES
+.BI "-f" " traj.xtc"
+.B Input
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-s" " topol.tpr"
+.B Input
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
+
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
+.BI "-ol" " bun_len.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-od" " bun_dist.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-ot" " bun_tilt.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-otr" " bun_tiltr.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-otl" " bun_tiltl.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-oa" " axes.pdb"
+.B Output, Opt.
+ Protein data bank file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " -1"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " -1"
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " -1"
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-na" " int" " 0"
+ Number of axes
+
+.BI "-[no]z" " no"
+ Use the Z-axis as reference iso the average axis
+
--- /dev/null
+.TH g_chi 1 "Tue 15 May 2001"
+.SH NAME
+g_chi
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3g_chi\fP
+.BI "-c" " conf.gro "
+.BI "-f" " traj.xtc "
+.BI "-o" " order.xvg "
+.BI "-p" " order.pdb "
+.BI "-ss" " ssdump.dat "
+.BI "-jc" " Jcoupling.xvg "
+.BI "-corr" " dihcorr.xvg "
+.BI "-g" " chi.log "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-[no]w" ""
+.BI "-r0" " int "
+.BI "-[no]phi" ""
+.BI "-[no]psi" ""
+.BI "-[no]omega" ""
+.BI "-[no]rama" ""
+.BI "-[no]viol" ""
+.BI "-[no]all" ""
+.BI "-[no]shift" ""
+.BI "-run" " int "
+.BI "-maxchi" " enum "
+.BI "-[no]normhisto" ""
+.BI "-[no]ramomega" ""
+.BI "-bfact" " real "
+.BI "-bmax" " real "
+.BI "-acflen" " int "
+.BI "-[no]normalize" ""
+.BI "-P" " enum "
+.BI "-fitfn" " enum "
+.BI "-ncskip" " int "
+.BI "-beginfit" " real "
+.BI "-endfit" " real "
+.SH DESCRIPTION
+g_chi computes phi, psi, omega and chi dihedrals for all your
+amino acid backbone and sidechains.
+It can compute dihedral angle as a function of time, and as
+histogram distributions.
+Output is in form of xvgr files, as well as a LaTeX table of the
+number of transitions per nanosecond.
+
+
+Order parameters S2 for each of the dihedrals are calculated and
+output as xvgr file and optionally as a pdb file with the S2
+values as B-factor.
+
+
+If option
+.B -c
+is given, the program will
+calculate dihedral autocorrelation functions. The function used
+is C(t) = cos(chi(tau)) cos(chi(tau+t)) . The use of cosines
+rather than angles themselves, resolves the problem of periodicity.
+(Van der Spoel & Berendsen (1997),
+.B Biophys. J. 72
+, 2032-2041).
+
+
+The option
+.B -r
+generates a contour plot of the average omega angle
+as a function of the phi and psi angles, that is, in a Ramachandran plot
+the average omega angle is plotted using color coding.
+.SH FILES
+.BI "-c" " conf.gro"
+.B Input
+ Generic structure: gro g96 pdb tpr tpb tpa
+
+.BI "-f" " traj.xtc"
+.B Input
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-o" " order.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-p" " order.pdb"
+.B Output, Opt.
+ Protein data bank file
+
+.BI "-ss" " ssdump.dat"
+.B Input, Opt.
+ Generic data file
+
+.BI "-jc" " Jcoupling.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-corr" " dihcorr.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-g" " chi.log"
+.B Output
+ Log file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " -1"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " -1"
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " -1"
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-[no]w" " no"
+ View output xvg, xpm, eps and pdb files
+
+.BI "-r0" " int" " 1"
+ starting residue
+
+.BI "-[no]phi" " no"
+ Output for Phi dihedral angles
+
+.BI "-[no]psi" " no"
+ Output for Psi dihedral angles
+
+.BI "-[no]omega" " no"
+ Output for Omega dihedrals (peptide bonds)
+
+.BI "-[no]rama" " no"
+ Generate Phi/Psi and Chi1/Chi2 ramachandran plots
+
+.BI "-[no]viol" " no"
+ Write a file that gives 0 or 1 for violated Ramachandran angles
+
+.BI "-[no]all" " no"
+ Output separate files for every dihedral.
+
+.BI "-[no]shift" " no"
+ Compute chemical shifts from Phi/Psi angles
+
+.BI "-run" " int" " 1"
+ perform running average over ndeg degrees for histograms
+
+.BI "-maxchi" " enum" " 0"
+ calculate first ndih Chi dihedrals: 0, 1, 2, 3, 4, 5 or 6
+
+.BI "-[no]normhisto" " yes"
+ Normalize histograms
+
+.BI "-[no]ramomega" " no"
+ compute average omega as a function of phi/psi and plot it in an xpm plot
+
+.BI "-bfact" " real" " -1"
+ B-factor value for pdb file for atoms with no calculated dihedral order parameter
+
+.BI "-bmax" " real" " 0"
+ Maximum B-factor on any of the atoms that make up a dihedral, for the dihedral angle to be considere in the statistics. Applies to database work where a number of X-Ray structures is analyzed. -bmax = 0 means no limit.
+
+.BI "-acflen" " int" " -1"
+ Length of the ACF, default is half the number of frames
+
+.BI "-[no]normalize" " yes"
+ Normalize ACF
+
+.BI "-P" " enum" " 0"
+ Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or 3
+
+.BI "-fitfn" " enum" " none"
+ Fit function: none, exp, aexp, exp_exp or vac
+
+.BI "-ncskip" " int" " 0"
+ Skip N points in the output file of correlation functions
+
+.BI "-beginfit" " real" " 0"
+ Time where to begin the exponential fit of the correlation function
+
+.BI "-endfit" " real" " -1"
+ Time where to end the exponential fit of the correlation function, -1 is till the end
+
+.SH DIAGNOSTICS
+\- Produces MANY output files (up to about 4 times the number of residues in the protein, twice that if autocorrelation functions are calculated). Typically several hundred files are output.
+
--- /dev/null
+.TH g_cluster 1 "Tue 15 May 2001"
+.SH NAME
+g_cluster
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3g_cluster\fP
+.BI "-f" " traj.xtc "
+.BI "-s" " topol.tpr "
+.BI "-n" " index.ndx "
+.BI "-dm" " rmsd.xpm "
+.BI "-o" " rmsd-clust.xpm "
+.BI "-g" " cluster.log "
+.BI "-dist" " rmsd-dist.xvg "
+.BI "-ev" " rmsd-eig.xvg "
+.BI "-sz" " clust-size.xvg "
+.BI "-tr" " clust-trans.xpm "
+.BI "-ntr" " clust-trans.xvg "
+.BI "-clid" " clust-id.xvg "
+.BI "-cl" " clusters.pdb "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-tu" " enum "
+.BI "-[no]w" ""
+.BI "-[no]dista" ""
+.BI "-nlevels" " int "
+.BI "-keepfree" " int "
+.BI "-cutoff" " real "
+.BI "-max" " real "
+.BI "-skip" " int "
+.BI "-[no]av" ""
+.BI "-wcl" " int "
+.BI "-nst" " int "
+.BI "-rmsmin" " real "
+.BI "-method" " enum "
+.BI "-[no]binary" ""
+.BI "-M" " int "
+.BI "-P" " int "
+.BI "-seed" " int "
+.BI "-niter" " int "
+.BI "-kT" " real "
+.SH DESCRIPTION
+g_cluster can cluster structures with several different methods.
+Distances between structures can be determined from a trajectory
+or read from an XPM matrix file with the
+.B -dm
+option.
+RMS deviation after fitting or RMS deviation of atom-pair distances
+can be used to define the distance between structures.
+
+
+full linkage: add a structure to a cluster when its distance to any
+element of the cluster is less than
+.B cutoff
+.
+
+
+Jarvis Patrick: add a structure to a cluster when this structure
+and a structure in the cluster have each other as neighbors and
+they have a least
+.B P
+neighbors in common. The neighbors
+of a structure are the M closest structures or all structures within
+
+.B cutoff
+.
+
+
+Monte Carlo: reorder the RMSD matrix using Monte Carlo.
+
+
+diagonalization: diagonalize the RMSD matrix.
+
+gromos: use algorithm as described in Daura
+.I et al.
+
+(
+.I Angew. Chem. Int. Ed.
+
+.B 1999
+,
+.I 38
+, pp 236-240).
+Count number of neighbors using cut-off, take structure with
+largest number of neighbors with all its neighbors as cluster
+and eleminate it from the pool of clusters. Repeat for remaining
+structures in pool.
+
+
+When the clustering algorithm assigns each structure to exactly one
+cluster (full linkage, Jarvis Patrick and gromos) and a trajectory
+file is supplied, the structure with
+the smallest average distance to the others or the average structure
+or all structures for each cluster will be written to a trajectory
+file. When writing all structures, separate numbered files are made
+for each cluster.
+.SH FILES
+.BI "-f" " traj.xtc"
+.B Input, Opt.
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-s" " topol.tpr"
+.B Input, Opt.
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
+
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
+.BI "-dm" " rmsd.xpm"
+.B Input, Opt.
+ X PixMap compatible matrix file
+
+.BI "-o" " rmsd-clust.xpm"
+.B Output
+ X PixMap compatible matrix file
+
+.BI "-g" " cluster.log"
+.B Output
+ Log file
+
+.BI "-dist" " rmsd-dist.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-ev" " rmsd-eig.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-sz" " clust-size.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-tr" " clust-trans.xpm"
+.B Output, Opt.
+ X PixMap compatible matrix file
+
+.BI "-ntr" " clust-trans.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-clid" " clust-id.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-cl" " clusters.pdb"
+.B Output, Opt.
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " -1"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " -1"
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " -1"
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-tu" " enum" " ps"
+ Time unit: ps, fs, ns, us, ms, s, m or h
+
+.BI "-[no]w" " no"
+ View output xvg, xpm, eps and pdb files
+
+.BI "-[no]dista" " no"
+ Use RMSD of distances instead of RMS deviation
+
+.BI "-nlevels" " int" " 40"
+ Discretize RMSD matrix in levels
+
+.BI "-keepfree" " int" " -4"
+ if 0 levels not to use when coloring clusters; if 0 nlevels/-keepfree+1 levels will not be used
+
+.BI "-cutoff" " real" " 0.1"
+ RMSD cut-off (nm) for two structures to be neighbor
+
+.BI "-max" " real" " -1"
+ Maximum level in RMSD matrix
+
+.BI "-skip" " int" " 1"
+ Only analyze every nr-th frame
+
+.BI "-[no]av" " no"
+ Write average iso middle structure for each cluster
+
+.BI "-wcl" " int" " 0"
+ Write all structures for first clusters to numbered files
+
+.BI "-nst" " int" " 1"
+ Only write all structures if more than per cluster
+
+.BI "-rmsmin" " real" " 0"
+ minimum rms difference with rest of cluster for writing structures
+
+.BI "-method" " enum" " linkage"
+ Method for cluster determination: linkage, jarvis-patrick, monte-carlo, diagonalization or gromos
+
+.BI "-[no]binary" " no"
+ Treat the RMSD matrix as consisting of 0 and 1, where the cut-off is given by -cutoff
+
+.BI "-M" " int" " 10"
+ Number of nearest neighbors considered for Jarvis-Patrick algorithm, 0 is use cutoff
+
+.BI "-P" " int" " 3"
+ Number of identical nearest neighbors required to form a cluster
+
+.BI "-seed" " int" " 1993"
+ Random number seed for Monte Carlo clustering algorithm
+
+.BI "-niter" " int" " 10000"
+ Number of iterations for MC
+
+.BI "-kT" " real" " 0.001"
+ Boltzmann weighting factor for Monte Carlo optimization (zero turns off uphill steps)
+
--- /dev/null
+.TH g_confrms 1 "Tue 15 May 2001"
+.SH NAME
+g_confrms
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3g_confrms\fP
+.BI "-f1" " conf1.gro "
+.BI "-f2" " conf2.gro "
+.BI "-o" " fit.pdb "
+.BI "-n1" " fit1.ndx "
+.BI "-n2" " fit2.ndx "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-[no]one" ""
+.BI "-[no]pbc" ""
+.SH DESCRIPTION
+g_confrms computes the root mean square deviation (RMSD) of two
+structures after LSQ fitting the second structure on the first one.
+The two structures do NOT need to have the same number of atoms,
+only the two index groups used for the fit need to be identical.
+
+
+
+The superimposed structures are written to file. In a
+.B .pdb
+file
+the two structures will be written as separate models
+(use
+.B rasmol -nmrpdb
+).
+.SH FILES
+.BI "-f1" " conf1.gro"
+.B Input
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
+
+.BI "-f2" " conf2.gro"
+.B Input
+ Generic structure: gro g96 pdb tpr tpb tpa
+
+.BI "-o" " fit.pdb"
+.B Output
+ Generic structure: gro g96 pdb
+
+.BI "-n1" " fit1.ndx"
+.B Input, Opt.
+ Index file
+
+.BI "-n2" " fit2.ndx"
+.B Input, Opt.
+ Index file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-[no]one" " no"
+ Only write the fitted structure to file
+
+.BI "-[no]pbc" " no"
+ Try to make molecules whole again
+
--- /dev/null
+.TH g_covar 1 "Tue 15 May 2001"
+.SH NAME
+g_covar
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3g_covar\fP
+.BI "-f" " traj.xtc "
+.BI "-s" " topol.tpr "
+.BI "-n" " index.ndx "
+.BI "-o" " eigenval.xvg "
+.BI "-v" " eigenvec.trr "
+.BI "-av" " average.pdb "
+.BI "-l" " covar.log "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-[no]fit" ""
+.BI "-[no]ref" ""
+.BI "-[no]mwa" ""
+.BI "-last" " int "
+.SH DESCRIPTION
+
+.B g_covar
+calculates and diagonalizes the (mass-weighted)
+covariance matrix.
+All structures are fitted to the structure in the structure file.
+When this is not a run input file periodicity will not be taken into
+account. When the fit and analysis groups are identical and the analysis
+is non mass-weighted, the fit will also be non mass-weighted.
+
+
+The eigenvectors are written to a trajectory file (
+.B -v
+).
+When the same atoms are used for the fit and the covariance analysis,
+the reference structure for the fit is written first with t=-1.
+The average (or reference when
+.B -ref
+is used) structure is
+written with t=0, the eigenvectors
+are written as frames with the eigenvector number as timestamp.
+
+
+The eigenvectors can be analyzed with
+.B g_anaeig
+.
+.SH FILES
+.BI "-f" " traj.xtc"
+.B Input
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-s" " topol.tpr"
+.B Input
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
+
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
+.BI "-o" " eigenval.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-v" " eigenvec.trr"
+.B Output
+ Full precision trajectory: trr trj
+
+.BI "-av" " average.pdb"
+.B Output
+ Generic structure: gro g96 pdb
+
+.BI "-l" " covar.log"
+.B Output
+ Log file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " -1"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " -1"
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " -1"
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-[no]fit" " yes"
+ Fit to a reference structure
+
+.BI "-[no]ref" " no"
+ Use the deviation from the conformation in the structure file instead of from the average
+
+.BI "-[no]mwa" " no"
+ Mass-weighted covariance analysis
+
+.BI "-last" " int" " -1"
+ Last eigenvector to write away (-1 is till the last)
+
--- /dev/null
+.TH g_density 1 "Tue 15 May 2001"
+.SH NAME
+g_density
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3g_density\fP
+.BI "-f" " traj.xtc "
+.BI "-n" " index.ndx "
+.BI "-s" " topol.tpr "
+.BI "-ei" " electrons.dat "
+.BI "-o" " density.xvg "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-[no]w" ""
+.BI "-d" " string "
+.BI "-sl" " int "
+.BI "-[no]number" ""
+.BI "-[no]ed" ""
+.BI "-[no]count" ""
+.SH DESCRIPTION
+Compute partial densities across the box, using an index file. Densities
+in gram/cubic centimeter, number densities or electron densities can be
+calculated. For electron densities, each atom is weighed by its atomic
+partial charge.
+.SH FILES
+.BI "-f" " traj.xtc"
+.B Input
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
+.BI "-s" " topol.tpr"
+.B Input
+ Generic run input: tpr tpb tpa
+
+.BI "-ei" " electrons.dat"
+.B Output
+ Generic data file
+
+.BI "-o" " density.xvg"
+.B Output
+ xvgr/xmgr file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " -1"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " -1"
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " -1"
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-[no]w" " no"
+ View output xvg, xpm, eps and pdb files
+
+.BI "-d" " string" " Z"
+ Take the normal on the membrane in direction X, Y or Z.
+
+.BI "-sl" " int" " 10"
+ Divide the box in nr slices.
+
+.BI "-[no]number" " no"
+ Calculate number density instead of mass density. Hydrogens are not counted!
+
+.BI "-[no]ed" " no"
+ Calculate electron density instead of mass density
+
+.BI "-[no]count" " no"
+ Only count atoms in slices, no densities. Hydrogens are not counted
+
+.SH DIAGNOSTICS
+\- When calculating electron densities, atomnames are used instead of types. This is bad.
+
+\- When calculating number densities, atoms with names that start with H are not counted. This may be surprising if you use hydrogens with names like OP3.
+
--- /dev/null
+.TH g_dielectric 1 "Tue 15 May 2001"
+.SH NAME
+g_dielectric
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3g_dielectric\fP
+.BI "-f" " Mtot.xvg "
+.BI "-d" " deriv.xvg "
+.BI "-o" " epsw.xvg "
+.BI "-c" " cole.xvg "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-[no]w" ""
+.BI "-[no]fft" ""
+.BI "-[no]x1" ""
+.BI "-eint" " real "
+.BI "-bfit" " real "
+.BI "-efit" " real "
+.BI "-tail" " real "
+.BI "-A" " real "
+.BI "-tau1" " real "
+.BI "-tau2" " real "
+.BI "-eps0" " real "
+.BI "-epsRF" " real "
+.BI "-fix" " int "
+.BI "-ffn" " enum "
+.BI "-nsmooth" " int "
+.SH DESCRIPTION
+dielectric calculates frequency dependent dielectric constants
+from the autocorrelation function of the total dipole moment in
+your simulation. This ACF can be generated by g_dipoles.
+For an estimate of the error you can run g_statistics on the
+ACF, and use the output thus generated for this program.
+The functional forms of the available functions are:
+
+
+One parmeter : y = Exp[-a1 x]
+Two parmeters : y = a2 Exp[-a1 x]
+Three parmeter: y = a2 Exp[-a1 x] + (1 - a2) Exp[-a3 x]
+Startvalues for the fit procedure can be given on the commandline.
+It is also possible to fix parameters at their start value, use -fix
+with the number of the parameter you want to fix.
+
+
+
+Three output files are generated, the first contains the ACF,
+an exponential fit to it with 1, 2 or 3 parameters, and the
+numerical derivative of the combination data/fit.
+The second file contains the real and imaginary parts of the
+frequency-dependent dielectric constant, the last gives a plot
+known as the Cole-Cole plot, in which the imaginary
+component is plotted as a function of the real component.
+For a pure exponential relaxation (Debye relaxation) the latter
+plot should be one half of a circle
+.SH FILES
+.BI "-f" " Mtot.xvg"
+.B Input
+ xvgr/xmgr file
+
+.BI "-d" " deriv.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-o" " epsw.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-c" " cole.xvg"
+.B Output
+ xvgr/xmgr file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " -1"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " -1"
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " -1"
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-[no]w" " no"
+ View output xvg, xpm, eps and pdb files
+
+.BI "-[no]fft" " no"
+ use fast fourier transform for correlation function
+
+.BI "-[no]x1" " yes"
+ use first column as X axis rather than first data set
+
+.BI "-eint" " real" " 5"
+ Time were to end the integration of the data and start to use the fit
+
+.BI "-bfit" " real" " 5"
+ Begin time of fit
+
+.BI "-efit" " real" " 500"
+ End time of fit
+
+.BI "-tail" " real" " 500"
+ Length of function including data and tail from fit
+
+.BI "-A" " real" " 0.5"
+ Start value for fit parameter A
+
+.BI "-tau1" " real" " 10"
+ Start value for fit parameter tau1
+
+.BI "-tau2" " real" " 1"
+ Start value for fit parameter tau2
+
+.BI "-eps0" " real" " 80"
+ Epsilon 0 of your liquid
+
+.BI "-epsRF" " real" " 78.5"
+ Epsilon of the reaction field used in your simulation. A value of 0 means infinity.
+
+.BI "-fix" " int" " 0"
+ Fix parameters at their start values, A (2), tau1 (1), or tau2 (4)
+
+.BI "-ffn" " enum" " none"
+ Fit function: none, exp, aexp, exp_exp or vac
+
+.BI "-nsmooth" " int" " 3"
+ Number of points for smoothing
+
--- /dev/null
+.TH g_dih 1 "Tue 15 May 2001"
+.SH NAME
+g_dih
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3g_dih\fP
+.BI "-f" " traj.xtc "
+.BI "-s" " topol.tpr "
+.BI "-o" " hello.out "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-[no]w" ""
+.BI "-[no]sa" ""
+.BI "-mult" " int "
+.SH DESCRIPTION
+g_dih can do two things. The default is to analyze dihedral transitions
+by merely computing all the dihedral angles defined in your topology
+for the whole trajectory. When a dihedral flips over to another minimum
+an angle/time plot is made.
+
+
+The opther option is to discretize the dihedral space into a number of
+bins, and group each conformation in dihedral space in the
+appropriate bin. The output is then given as a number of dihedral
+conformations sorted according to occupancy.
+.SH FILES
+.BI "-f" " traj.xtc"
+.B Input
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-s" " topol.tpr"
+.B Input
+ Generic run input: tpr tpb tpa
+
+.BI "-o" " hello.out"
+.B Output
+ Generic output file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " -1"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " -1"
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " -1"
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-[no]w" " no"
+ View output xvg, xpm, eps and pdb files
+
+.BI "-[no]sa" " no"
+ Perform cluster analysis in dihedral space instead of analysing dihedral transitions.
+
+.BI "-mult" " int" " -1"
+ mulitiplicity for dihedral angles (by default read from topology)
+
+.SH DIAGNOSTICS
+\- should not ask for number of frames
+
--- /dev/null
+.TH g_dipoles 1 "Tue 15 May 2001"
+.SH NAME
+g_dipoles
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3g_dipoles\fP
+.BI "-enx" " ener.edr "
+.BI "-f" " traj.xtc "
+.BI "-s" " topol.tpr "
+.BI "-n" " index.ndx "
+.BI "-o" " Mtot.xvg "
+.BI "-e" " epsilon.xvg "
+.BI "-a" " aver.xvg "
+.BI "-d" " dipdist.xvg "
+.BI "-c" " dipcorr.xvg "
+.BI "-g" " gkr.xvg "
+.BI "-q" " quadrupole.xvg "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-[no]w" ""
+.BI "-mu" " real "
+.BI "-mumax" " real "
+.BI "-epsilonRF" " real "
+.BI "-skip" " int "
+.BI "-temp" " real "
+.BI "-[no]avercorr" ""
+.BI "-gkratom" " int "
+.BI "-acflen" " int "
+.BI "-[no]normalize" ""
+.BI "-P" " enum "
+.BI "-fitfn" " enum "
+.BI "-ncskip" " int "
+.BI "-beginfit" " real "
+.BI "-endfit" " real "
+.SH DESCRIPTION
+g_dipoles computes the total dipole plus fluctuations of a simulation
+system. From this you can compute e.g. the dielectric constant for
+low dielectric media
+
+
+The file dip.xvg contains the total dipole moment of a frame, the
+components as well as the norm of the vector.
+The file aver.xvg contains |Mu|2 and |Mu| 2 during the
+simulation.
+The file dip.xvg contains the distribution of dipole moments during
+the simulation
+The mu_max is used as the highest value in the distribution graph.
+
+
+Furthermore the dipole autocorrelation function will be computed, when
+option -c is used. It can be averaged over all molecules,
+or (with option -avercorr) it can be computed as the autocorrelation
+of the total dipole moment of the simulation box.
+
+
+At the moment the dielectric constant is calculated only correct if
+a rectangular or cubic simulation box is used.
+
+
+Option
+.B -g
+produces a plot of the distance dependent Kirkwood
+G-factor, as well as the average cosine of the angle between the dipoles
+as a function of the distance. The plot also includes gOO and hOO
+according to Nymand & Linse, JCP 112 (2000) pp 6386-6395.
+
+
+
+
+
+EXAMPLES
+
+
+g_dipoles -P1 -n mols -o dip_sqr -mu 2.273 -mumax 5.0
+-nofft
+
+
+This will calculate the autocorrelation function of the molecular
+dipoles using a first order Legendre polynomial of the angle of the
+dipole vector and itself a time t later. For this calculation 1001
+frames will be used. Further the dielectric constant will be calculated
+using an epsilonRF of infinity (default), temperature of 300 K (default) and
+an average dipole moment of the molecule of 2.273 (SPC). For the
+distribution function a maximum of 5.0 will be used.
+.SH FILES
+.BI "-enx" " ener.edr"
+.B Input, Opt.
+ Generic energy: edr ene
+
+.BI "-f" " traj.xtc"
+.B Input
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-s" " topol.tpr"
+.B Input
+ Generic run input: tpr tpb tpa
+
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
+.BI "-o" " Mtot.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-e" " epsilon.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-a" " aver.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-d" " dipdist.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-c" " dipcorr.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-g" " gkr.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-q" " quadrupole.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " -1"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " -1"
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " -1"
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-[no]w" " no"
+ View output xvg, xpm, eps and pdb files
+
+.BI "-mu" " real" " -1"
+ dipole of a single molecule (in Debye)
+
+.BI "-mumax" " real" " 5"
+ max dipole in Debye (for histrogram)
+
+.BI "-epsilonRF" " real" " 0"
+ epsilon of the reaction field used during the simulation, needed for dieclectric constant calculation. WARNING: 0.0 means infinity (default)
+
+.BI "-skip" " int" " 0"
+ Skip steps in the output (but not in the computations)
+
+.BI "-temp" " real" " 300"
+ average temperature of the simulation (needed for dielectric constant calculation)
+
+.BI "-[no]avercorr" " no"
+ calculate AC function of average dipole moment of the simulation box rather than average of AC function per molecule
+
+.BI "-gkratom" " int" " 0"
+ Use the n-th atom of a molecule (starting from 1) to calculate the distance between molecules rather than the center of charge (when 0) in the calculation of distance dependent Kirkwood factors
+
+.BI "-acflen" " int" " -1"
+ Length of the ACF, default is half the number of frames
+
+.BI "-[no]normalize" " yes"
+ Normalize ACF
+
+.BI "-P" " enum" " 0"
+ Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or 3
+
+.BI "-fitfn" " enum" " none"
+ Fit function: none, exp, aexp, exp_exp or vac
+
+.BI "-ncskip" " int" " 0"
+ Skip N points in the output file of correlation functions
+
+.BI "-beginfit" " real" " 0"
+ Time where to begin the exponential fit of the correlation function
+
+.BI "-endfit" " real" " -1"
+ Time where to end the exponential fit of the correlation function, -1 is till the end
+
--- /dev/null
+.TH g_disre 1 "Tue 15 May 2001"
+.SH NAME
+g_disre
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3g_disre\fP
+.BI "-s" " topol.tpr "
+.BI "-f" " traj.xtc "
+.BI "-ds" " drsum.xvg "
+.BI "-da" " draver.xvg "
+.BI "-dn" " drnum.xvg "
+.BI "-dm" " drmax.xvg "
+.BI "-dr" " restr.xvg "
+.BI "-l" " disres.log "
+.BI "-n" " viol.ndx "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-[no]w" ""
+.BI "-ntop" " int "
+.SH DESCRIPTION
+g_disre computes violations of distance restraints. If necessary
+all protons can be added to a protein molecule. The program allways
+computes the instantaneous violations rather than time-averaged,
+because this analysis is done from a trajectory file afterwards
+it does not make sense to use time averaging.
+
+
+An index file may be used to select specific restraints for
+printing.
+.SH FILES
+.BI "-s" " topol.tpr"
+.B Input
+ Generic run input: tpr tpb tpa
+
+.BI "-f" " traj.xtc"
+.B Input
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-ds" " drsum.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-da" " draver.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-dn" " drnum.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-dm" " drmax.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-dr" " restr.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-l" " disres.log"
+.B Output
+ Log file
+
+.BI "-n" " viol.ndx"
+.B Input, Opt.
+ Index file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " -1"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " -1"
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " -1"
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-[no]w" " no"
+ View output xvg, xpm, eps and pdb files
+
+.BI "-ntop" " int" " 6"
+ Number of large violations that are stored in the log file every step
+
--- /dev/null
+.TH g_dist 1 "Tue 15 May 2001"
+.SH NAME
+g_dist
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3g_dist\fP
+.BI "-f" " traj.xtc "
+.BI "-s" " topol.tpr "
+.BI "-n" " index.ndx "
+.BI "-o" " dist.xvg "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-dist" " real "
+.SH DESCRIPTION
+g_dist can calculate the distance between the centers of mass of two
+groups of atoms as a function of time. The total distance and its
+x, y and z components are plotted.
+
+
+Or when
+.B -dist
+is set, print all the atoms in group 2 that are
+closer than a certain distance to the center of mass of group 1.
+.SH FILES
+.BI "-f" " traj.xtc"
+.B Input
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-s" " topol.tpr"
+.B Input
+ Generic run input: tpr tpb tpa
+
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
+.BI "-o" " dist.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " -1"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " -1"
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " -1"
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-dist" " real" " 0"
+ Print all atoms in group 2 closer than dist to the center of mass of group 1
+
--- /dev/null
+.TH g_dyndom 1 "Tue 15 May 2001"
+.SH NAME
+g_dyndom
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3g_dyndom\fP
+.BI "-f" " dyndom.pdb "
+.BI "-o" " rotated.xtc "
+.BI "-n" " domains.ndx "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-firstangle" " real "
+.BI "-lastangle" " real "
+.BI "-nframe" " int "
+.BI "-maxangle" " real "
+.BI "-trans" " real "
+.BI "-head" " vector "
+.BI "-tail" " vector "
+.SH DESCRIPTION
+g_dyndom reads a pdb file output from DynDom
+http://md.chem.rug.nl/~steve/DynDom/dyndom.home.html
+It reads the coordinates, and the coordinates of the rotation axis
+furthermore it reads an index file containing the domains.
+Furthermore it takes the first and last atom of the arrow file
+as command line arguments (head and tail) and
+finally it takes the translation vector (given in DynDom info file)
+and the angle of rotation (also as command line arguments). If the angle
+determined by DynDom is given, one should be able to recover the
+second structure used for generating the DynDom output.
+Because of limited numerical accuracy this should be verified by
+computing an all-atom RMSD (using
+.B g_confrms
+) rather than by file
+comparison (using diff).
+
+
+The purpose of this program is to interpolate and extrapolate the
+rotation as found by DynDom. As a result unphysical structures with
+long or short bonds, or overlapping atoms may be produced. Visual
+inspection, and energy minimization may be necessary to
+validate the structure.
+.SH FILES
+.BI "-f" " dyndom.pdb"
+.B Input
+ Protein data bank file
+
+.BI "-o" " rotated.xtc"
+.B Output
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-n" " domains.ndx"
+.B Input
+ Index file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 0"
+ Set the nicelevel
+
+.BI "-firstangle" " real" " 0"
+ Angle of rotation about rotation vector
+
+.BI "-lastangle" " real" " 0"
+ Angle of rotation about rotation vector
+
+.BI "-nframe" " int" " 11"
+ Number of steps on the pathway
+
+.BI "-maxangle" " real" " 0"
+ DymDom dtermined angle of rotation about rotation vector
+
+.BI "-trans" " real" " 0"
+ Translation (Aangstroem) along rotation vector (see DynDom info file)
+
+.BI "-head" " vector" " 0 0 0"
+ First atom of the arrow vector
+
+.BI "-tail" " vector" " 0 0 0"
+ Last atom of the arrow vector
+
--- /dev/null
+.TH g_enemat 1 "Tue 15 May 2001"
+.SH NAME
+g_enemat
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3g_enemat\fP
+.BI "-f" " ener.edr "
+.BI "-groups" " groups.dat "
+.BI "-eref" " eref.dat "
+.BI "-emat" " emat.xpm "
+.BI "-etot" " energy.xvg "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-[no]w" ""
+.BI "-[no]sum" ""
+.BI "-skip" " int "
+.BI "-[no]mean" ""
+.BI "-nlevels" " int "
+.BI "-max" " real "
+.BI "-min" " real "
+.BI "-[no]coul" ""
+.BI "-[no]coulr" ""
+.BI "-[no]coul14" ""
+.BI "-[no]lj" ""
+.BI "-[no]lj14" ""
+.BI "-[no]bham" ""
+.BI "-[no]free" ""
+.BI "-temp" " real "
+.SH DESCRIPTION
+g_enemat extracts an energy matrix from an energy file.
+With
+.B -groups
+a file must be supplied with on each
+line a group to be used. For these groups a matrices of
+interaction energies will be calculated. Also the total
+interaction energy energy per group is calculated.
+
+
+An approximation of the free energy is calculated using:
+E(free) = E0 + kT log( exp((E-E0)/kT) ), where ''
+stands for time-average. A file with reference free energies
+can be supplied to calculate the free energy difference
+with some reference state. Group names (e.g. residue names
+in the reference file should correspond to the group names
+as used in the
+.B -groups
+file, but a appended number
+(e.g. residue number)in the
+.B -groups
+will be ignored
+in the comparison.
+.SH FILES
+.BI "-f" " ener.edr"
+.B Input, Opt.
+ Generic energy: edr ene
+
+.BI "-groups" " groups.dat"
+.B Input
+ Generic data file
+
+.BI "-eref" " eref.dat"
+.B Input, Opt.
+ Generic data file
+
+.BI "-emat" " emat.xpm"
+.B Output
+ X PixMap compatible matrix file
+
+.BI "-etot" " energy.xvg"
+.B Output
+ xvgr/xmgr file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " -1"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " -1"
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " -1"
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-[no]w" " no"
+ View output xvg, xpm, eps and pdb files
+
+.BI "-[no]sum" " no"
+ Sum the energy terms selected rather than display them all
+
+.BI "-skip" " int" " 0"
+ Skip number of frames between data points
+
+.BI "-[no]mean" " yes"
+ with -groups calculates matrix of mean energies in stead of matrix for each timestep
+
+.BI "-nlevels" " int" " 20"
+ number of levels for matrix colors
+
+.BI "-max" " real" " 1e+20"
+ max value for energies
+
+.BI "-min" " real" " -1e+20"
+ min value for energies
+
+.BI "-[no]coul" " yes"
+ calculate Coulomb SR energies
+
+.BI "-[no]coulr" " no"
+ calculate Coulomb LR energies
+
+.BI "-[no]coul14" " no"
+ calculate Coulomb 1-4 energies
+
+.BI "-[no]lj" " yes"
+ calculate Lennard-Jones SR energies
+
+.BI "-[no]lj14" " no"
+ calculate Lennard-Jones 1-4 energies
+
+.BI "-[no]bham" " no"
+ calculate Buckingham energies
+
+.BI "-[no]free" " yes"
+ calculate free energy
+
+.BI "-temp" " real" " 300"
+ reference temperature for free energy calculation
+
--- /dev/null
+.TH g_energy 1 "Tue 15 May 2001"
+.SH NAME
+g_energy
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3g_energy\fP
+.BI "-f" " ener.edr "
+.BI "-f2" " ener.edr "
+.BI "-s" " topol.tpr "
+.BI "-o" " energy.xvg "
+.BI "-viol" " violaver.xvg "
+.BI "-pairs" " pairs.xvg "
+.BI "-corr" " enecorr.xvg "
+.BI "-vis" " visco.xvg "
+.BI "-ravg" " runavgdf.xvg "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-[no]w" ""
+.BI "-[no]fee" ""
+.BI "-fetemp" " real "
+.BI "-zero" " real "
+.BI "-[no]sum" ""
+.BI "-[no]dp" ""
+.BI "-[no]mutot" ""
+.BI "-skip" " int "
+.BI "-[no]aver" ""
+.BI "-nmol" " int "
+.BI "-ndf" " int "
+.BI "-[no]fluc" ""
+.BI "-acflen" " int "
+.BI "-[no]normalize" ""
+.BI "-P" " enum "
+.BI "-fitfn" " enum "
+.BI "-ncskip" " int "
+.BI "-beginfit" " real "
+.BI "-endfit" " real "
+.SH DESCRIPTION
+g_energy extracts energy components or distance restraint
+data from an energy file. The user is prompted to interactively
+select the energy terms she wants.
+
+
+When the
+.B -viol
+option is set, the time averaged
+violations are plotted and the running time-averaged and
+instantaneous sum of violations are recalculated. Additionally
+running time-averaged and instantaneous distances between
+selected pairs can be plotted with the
+.B -pairs
+option.
+
+
+Average and RMSD are calculated with full precision from the
+simulation (see printed manual). Drift is calculated by performing
+a LSQ fit of the data to a straight line. Total drift is drift
+multiplied by total time.
+
+
+With
+.B -fee
+a free energy estimate is calculated using
+the formula: G = -ln e (E/kT) * kT, where k is Boltzmann's
+constant, T is set by
+.B -fetemp
+and the average is over the
+ensemble (or time in a trajectory). Note that this is in principle
+only correct when averaging over the whole (Boltzmann) ensemble
+and using the potential energy. This also allows for an entropy
+estimate using G = H - T S, where H is the enthalpy (H = U + p V)
+and S entropy.
+
+
+When a second energy file is specified (
+.B -f2
+), a free energy
+difference is calculated dF = -kT ln e -(EB-EA)/kT A ,
+where EA and EB are the energies from the first and second energy
+files, and the average is over the ensemble A.
+.B NOTE
+that
+the energies must both be calculated from the same trajectory.
+.SH FILES
+.BI "-f" " ener.edr"
+.B Input
+ Generic energy: edr ene
+
+.BI "-f2" " ener.edr"
+.B Input, Opt.
+ Generic energy: edr ene
+
+.BI "-s" " topol.tpr"
+.B Input, Opt.
+ Generic run input: tpr tpb tpa
+
+.BI "-o" " energy.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-viol" " violaver.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-pairs" " pairs.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-corr" " enecorr.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-vis" " visco.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-ravg" " runavgdf.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " -1"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " -1"
+ Last frame (ps) to read from trajectory
+
+.BI "-[no]w" " no"
+ View output xvg, xpm, eps and pdb files
+
+.BI "-[no]fee" " no"
+ Do a free energy estimate
+
+.BI "-fetemp" " real" " 300"
+ Reference temperature for free energy calculation
+
+.BI "-zero" " real" " 0"
+ Subtract a zero-point energy
+
+.BI "-[no]sum" " no"
+ Sum the energy terms selected rather than display them all
+
+.BI "-[no]dp" " no"
+ Print energies in high precision
+
+.BI "-[no]mutot" " no"
+ Compute the total dipole moment from the components
+
+.BI "-skip" " int" " 0"
+ Skip number of frames between data points
+
+.BI "-[no]aver" " no"
+ Print also the X1,t and sigma1,t, only if only 1 energy is requested
+
+.BI "-nmol" " int" " 1"
+ Number of molecules in your sample: the energies are divided by this number
+
+.BI "-ndf" " int" " 3"
+ Number of degrees of freedom per molecule. Necessary for calculating the heat capacity
+
+.BI "-[no]fluc" " no"
+ Calculate autocorrelation of energy fluctuations rather than energy itself
+
+.BI "-acflen" " int" " -1"
+ Length of the ACF, default is half the number of frames
+
+.BI "-[no]normalize" " yes"
+ Normalize ACF
+
+.BI "-P" " enum" " 0"
+ Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or 3
+
+.BI "-fitfn" " enum" " none"
+ Fit function: none, exp, aexp, exp_exp or vac
+
+.BI "-ncskip" " int" " 0"
+ Skip N points in the output file of correlation functions
+
+.BI "-beginfit" " real" " 0"
+ Time where to begin the exponential fit of the correlation function
+
+.BI "-endfit" " real" " -1"
+ Time where to end the exponential fit of the correlation function, -1 is till the end
+
--- /dev/null
+.TH g_gyrate 1 "Tue 15 May 2001"
+.SH NAME
+g_gyrate
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3g_gyrate\fP
+.BI "-f" " traj.xtc "
+.BI "-s" " topol.tpr "
+.BI "-o" " gyrate.xvg "
+.BI "-n" " index.ndx "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-[no]w" ""
+.BI "-[no]q" ""
+.BI "-[no]p" ""
+.SH DESCRIPTION
+g_gyrate computes the radius of gyration of a group of atoms
+and the radii of gyration about the x, y and z axes,as a function of time. The atoms are explicitly mass weighted.
+.SH FILES
+.BI "-f" " traj.xtc"
+.B Input
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-s" " topol.tpr"
+.B Input
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
+
+.BI "-o" " gyrate.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " -1"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " -1"
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " -1"
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-[no]w" " no"
+ View output xvg, xpm, eps and pdb files
+
+.BI "-[no]q" " no"
+ Use absolute value of the charge of an atom as weighting factor instead of mass
+
+.BI "-[no]p" " no"
+ Calculate the radii of gyration about the principal axes.
+
--- /dev/null
+.TH g_h2order 1 "Tue 15 May 2001"
+.SH NAME
+g_h2order
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3g_h2order\fP
+.BI "-f" " traj.xtc "
+.BI "-n" " index.ndx "
+.BI "-nm" " index.ndx "
+.BI "-s" " topol.tpr "
+.BI "-o" " order.xvg "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-[no]w" ""
+.BI "-d" " string "
+.BI "-sl" " int "
+.SH DESCRIPTION
+Compute the orientation of water molecules with respect to the normal
+of the box. The program determines the average cosine of the angle
+between de dipole moment of water and an axis of the box. The box is
+divided in slices and the average orientation per slice is printed.
+Each water molecule is assigned to a slice, per time frame, based on the
+position of the oxygen. When -nm is used the angle between the water
+dipole and the axis from the center of mass to the oxygen is calculated
+instead of the angle between the dipole and a box axis.
+.SH FILES
+.BI "-f" " traj.xtc"
+.B Input
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-n" " index.ndx"
+.B Input
+ Index file
+
+.BI "-nm" " index.ndx"
+.B Input, Opt.
+ Index file
+
+.BI "-s" " topol.tpr"
+.B Input
+ Generic run input: tpr tpb tpa
+
+.BI "-o" " order.xvg"
+.B Output
+ xvgr/xmgr file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " -1"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " -1"
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " -1"
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-[no]w" " no"
+ View output xvg, xpm, eps and pdb files
+
+.BI "-d" " string" " Z"
+ Take the normal on the membrane in direction X, Y or Z.
+
+.BI "-sl" " int" " 0"
+ Calculate order parameter as function of boxlength, dividing the box in nr slices.
+
+.SH DIAGNOSTICS
+\- The program assigns whole water molecules to a slice, based on the firstatom of three in the index file group. It assumes an order O,H,H.Name is not important, but the order is. If this demand is not met,assigning molecules to slices is different.
+
--- /dev/null
+.TH g_hbond 1 "Tue 15 May 2001"
+.SH NAME
+g_hbond
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3g_hbond\fP
+.BI "-f" " traj.xtc "
+.BI "-s" " topol.tpr "
+.BI "-n" " index.ndx "
+.BI "-g" " hbond.log "
+.BI "-sel" " select.ndx "
+.BI "-num" " hbnum.xvg "
+.BI "-ac" " hbac.xvg "
+.BI "-dist" " hbdist.xvg "
+.BI "-ang" " hbang.xvg "
+.BI "-hx" " hbhelix.xvg "
+.BI "-hbn" " hbond.ndx "
+.BI "-hbm" " hbmap.xpm "
+.BI "-da" " danum.xvg "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-[no]ins" ""
+.BI "-a" " real "
+.BI "-r" " real "
+.BI "-abin" " real "
+.BI "-rbin" " real "
+.BI "-[no]nitacc" ""
+.BI "-shell" " real "
+.SH DESCRIPTION
+g_hbond computes and analyzes hydrogen bonds. Hydrogen bonds are
+determined based on cutoffs for the angle Donor - Hydrogen - Acceptor
+(zero is extended) and the distance Hydrogen - Acceptor.
+OH and NH groups are regarded as donors, O is an acceptor always,
+N is an acceptor by default, but this can be switched using
+
+.B -nitacc
+. Dummy hydrogen atoms are assumed to be connected
+to the first preceding non-hydrogen atom.
+
+
+You need to specify two groups for analysis, which must be either
+identical or non-overlapping. All hydrogen bonds between the two
+groups are analyzed.
+
+
+If you set -shell, you will be asked for an additional index group
+which should contain exactly one atom. In this case, only hydrogen
+bonds between atoms within the shell distance from the one atom are
+considered.
+
+It is also possible to analyse specific hydrogen bonds with
+
+.B -sel
+. This index file must contain a group of atom triplets
+Donor Hydrogen Acceptor, in the following way:
+
+
+
+.B
+[ selected ]
+
+ 20 21 24
+
+ 25 26 29
+
+ 1 3 6
+
+
+
+
+Note that the triplets need not be on separate lines.
+Each atom triplet specifies a hydrogen bond to be analyzed,
+note also that no check is made for the types of atoms.
+
+
+
+.B -ins
+turns on computing solvent insertion into hydrogen bonds.
+In this case an additional group must be selected, specifying the
+solvent molecules.
+
+
+
+.B Output:
+
+
+
+.B -num
+: number of hydrogen bonds as a function of time.
+
+
+.B -ac
+: average over all autocorrelations of the existence
+functions (either 0 or 1) of all hydrogen bonds.
+
+
+.B -dist
+: distance distribution of all hydrogen bonds.
+
+
+.B -ang
+: angle distribution of all hydrogen bonds.
+
+
+.B -hx
+: the number of n-n+i hydrogen bonds as a function of time
+where n and n+i stand for residue numbers and i ranges from 0 to 6.
+This includes the n-n+3, n-n+4 and n-n+5 hydrogen bonds associated
+with helices in proteins.
+
+
+.B -hbn
+: all selected groups, donors, hydrogens and acceptors
+for selected groups, all hydrogen bonded atoms from all groups and
+all solvent atoms involved in insertion.
+
+
+.B -hbm
+: existence matrix for all hydrogen bonds over all
+frames, this also contains information on solvent insertion
+into hydrogen bonds. Ordering is identical to that in
+.B -hbn
+
+index file.
+
+
+.B -da
+: write out the number of donors and acceptors analyzed for
+each timeframe. This is especially usefull when using
+.B -shell
+.
+.SH FILES
+.BI "-f" " traj.xtc"
+.B Input
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-s" " topol.tpr"
+.B Input
+ Generic run input: tpr tpb tpa
+
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
+.BI "-g" " hbond.log"
+.B Output, Opt.
+ Log file
+
+.BI "-sel" " select.ndx"
+.B Input, Opt.
+ Index file
+
+.BI "-num" " hbnum.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-ac" " hbac.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-dist" " hbdist.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-ang" " hbang.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-hx" " hbhelix.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-hbn" " hbond.ndx"
+.B Output, Opt.
+ Index file
+
+.BI "-hbm" " hbmap.xpm"
+.B Output, Opt.
+ X PixMap compatible matrix file
+
+.BI "-da" " danum.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " -1"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " -1"
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " -1"
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-[no]ins" " no"
+ Analyze solvent insertion
+
+.BI "-a" " real" " 60"
+ Cutoff angle (degrees, Donor - Hydrogen - Acceptor)
+
+.BI "-r" " real" " 0.25"
+ Cutoff radius (nm, Hydrogen - Acceptor)
+
+.BI "-abin" " real" " 1"
+ Binwidth angle distribution (degrees)
+
+.BI "-rbin" " real" " 0.005"
+ Binwidth distance distribution (nm)
+
+.BI "-[no]nitacc" " yes"
+ Regard nitrogen atoms as acceptors
+
+.BI "-shell" " real" " -1"
+ when 0, only calculate hydrogen bonds within nm shell around one particle
+
--- /dev/null
+.TH g_helix 1 "Tue 15 May 2001"
+.SH NAME
+g_helix
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3g_helix\fP
+.BI "-s" " topol.tpr "
+.BI "-n" " index.ndx "
+.BI "-f" " traj.xtc "
+.BI "-to" " gtraj.g87 "
+.BI "-cz" " zconf.gro "
+.BI "-co" " waver.gro "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-[no]w" ""
+.BI "-r0" " int "
+.BI "-[no]q" ""
+.BI "-[no]F" ""
+.BI "-[no]db" ""
+.BI "-[no]ev" ""
+.BI "-ahxstart" " int "
+.BI "-ahxend" " int "
+.SH DESCRIPTION
+g_helix computes all kind of helix properties. First, the peptide
+is checked to find the longest helical part. This is determined by
+Hydrogen bonds and Phi/Psi angles.
+That bit is fitted
+to an ideal helix around the Z-axis and centered around the origin.
+Then the following properties are computed:
+
+
+
+.B 1.
+Helix radius (file radius.xvg). This is merely the
+RMS deviation in two dimensions for all Calpha atoms.
+it is calced as sqrt((SUM i(x2(i)+y2(i)))/N), where N is the number
+of backbone atoms. For an ideal helix the radius is 0.23 nm
+
+
+.B 2.
+Twist (file twist.xvg). The average helical angle per
+residue is calculated. For alpha helix it is 100 degrees,
+for 3-10 helices it will be smaller,
+for 5-helices it will be larger.
+
+
+.B 3.
+Rise per residue (file rise.xvg). The helical rise per
+residue is plotted as the difference in Z-coordinate between Ca
+atoms. For an ideal helix this is 0.15 nm
+
+
+.B 4.
+Total helix length (file len-ahx.xvg). The total length
+of the
+helix in nm. This is simply the average rise (see above) times the
+number of helical residues (see below).
+
+
+.B 5.
+Number of helical residues (file n-ahx.xvg). The title says
+it all.
+
+
+.B 6.
+Helix Dipole, backbone only (file dip-ahx.xvg).
+
+
+.B 7.
+RMS deviation from ideal helix, calculated for the Calpha
+atoms only (file rms-ahx.xvg).
+
+
+.B 8.
+Average Calpha-Calpha dihedral angle (file phi-ahx.xvg).
+
+
+.B 9.
+Average Phi and Psi angles (file phipsi.xvg).
+
+
+.B 10.
+Ellipticity at 222 nm according to
+.I Hirst and Brooks
+
+
+
+
+.SH FILES
+.BI "-s" " topol.tpr"
+.B Input
+ Generic run input: tpr tpb tpa
+
+.BI "-n" " index.ndx"
+.B Input
+ Index file
+
+.BI "-f" " traj.xtc"
+.B Input
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-to" " gtraj.g87"
+.B Output, Opt.
+ Gromos-87 ASCII trajectory format
+
+.BI "-cz" " zconf.gro"
+.B Output
+ Generic structure: gro g96 pdb
+
+.BI "-co" " waver.gro"
+.B Output
+ Generic structure: gro g96 pdb
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " -1"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " -1"
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " -1"
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-[no]w" " no"
+ View output xvg, xpm, eps and pdb files
+
+.BI "-r0" " int" " 1"
+ The first residue number in the sequence
+
+.BI "-[no]q" " no"
+ Check at every step which part of the sequence is helical
+
+.BI "-[no]F" " yes"
+ Toggle fit to a perfect helix
+
+.BI "-[no]db" " no"
+ Print debug info
+
+.BI "-[no]ev" " no"
+ Write a new 'trajectory' file for ED
+
+.BI "-ahxstart" " int" " 0"
+ First residue in helix
+
+.BI "-ahxend" " int" " 0"
+ Last residue in helix
+
--- /dev/null
+.TH g_lie 1 "Tue 15 May 2001"
+.SH NAME
+g_lie
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3g_lie\fP
+.BI "-f" " ener.edr "
+.BI "-o" " lie.xvg "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-[no]w" ""
+.BI "-Elj" " real "
+.BI "-Eqq" " real "
+.BI "-Clj" " real "
+.BI "-Cqq" " real "
+.BI "-ligand" " string "
+.SH DESCRIPTION
+g_lie computes a free energy estimate based on an energy analysis
+from. One needs an energy file with the following components:
+Coul (A-B) LJ-SR (A-B) etc.
+.SH FILES
+.BI "-f" " ener.edr"
+.B Input
+ Generic energy: edr ene
+
+.BI "-o" " lie.xvg"
+.B Output
+ xvgr/xmgr file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-[no]w" " no"
+ View output xvg, xpm, eps and pdb files
+
+.BI "-Elj" " real" " 0"
+ Lennard-Jones interaction between ligand and solvent
+
+.BI "-Eqq" " real" " 0"
+ Coulomb interaction between ligand and solvent
+
+.BI "-Clj" " real" " 0.181"
+ Factor in the LIE equation for Lennard-Jones component of energy
+
+.BI "-Cqq" " real" " 0"
+ Factor in the LIE equation for Coulomb component of energy
+
+.BI "-ligand" " string" " "
+ Name of the ligand in the energy file
+
--- /dev/null
+.TH g_mdmat 1 "Tue 15 May 2001"
+.SH NAME
+g_mdmat
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3g_mdmat\fP
+.BI "-f" " traj.xtc "
+.BI "-s" " topol.tpr "
+.BI "-n" " index.ndx "
+.BI "-mean" " dm.xpm "
+.BI "-frames" " dmf.xpm "
+.BI "-no" " num.xvg "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-t" " real "
+.BI "-nlevels" " int "
+.SH DESCRIPTION
+g_mdmat makes distance matrices consisting of the smallest distance
+between residue pairs. With -frames these distance matrices can be
+stored as a function
+of time, to be able to see differences in tertiary structure as a
+funcion of time. If you choose your options unwise, this may generate
+a large output file. Default only an averaged matrix over the whole
+trajectory is output.
+Also a count of the number of different atomic contacts between
+residues over the whole trajectory can be made.
+The output can be processed with xpm2ps to make a PostScript (tm) plot.
+.SH FILES
+.BI "-f" " traj.xtc"
+.B Input
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-s" " topol.tpr"
+.B Input
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
+
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
+.BI "-mean" " dm.xpm"
+.B Output
+ X PixMap compatible matrix file
+
+.BI "-frames" " dmf.xpm"
+.B Output, Opt.
+ X PixMap compatible matrix file
+
+.BI "-no" " num.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " -1"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " -1"
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " -1"
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-t" " real" " 1.5"
+ trunc distance
+
+.BI "-nlevels" " int" " 40"
+ Discretize distance in levels
+
--- /dev/null
+.TH g_mindist 1 "Tue 15 May 2001"
+.SH NAME
+g_mindist
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3g_mindist\fP
+.BI "-f" " traj.xtc "
+.BI "-s" " topol.tpr "
+.BI "-n" " index.ndx "
+.BI "-od" " mindist.xvg "
+.BI "-on" " numcont.xvg "
+.BI "-o" " atm-pair.out "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-[no]w" ""
+.BI "-[no]matrix" ""
+.BI "-d" " real "
+.BI "-[no]pi" ""
+.SH DESCRIPTION
+g_mindist computes the distance between one group and a number of
+other groups.
+Both the minimum distance and the number of contacts within a given
+distance are written to two separate output files.
+
+
+With option
+.B -pi
+the minimum distance of a group to its
+periodic image is plotted. This is useful for checking if a protein
+has seen its periodic image during a simulation. Only one shift in
+each direction is considered, giving a total of 26 shifts.
+It also plots the maximum distance within the group and the lengths
+of the three box vectors.
+This option is very slow.
+.SH FILES
+.BI "-f" " traj.xtc"
+.B Input
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-s" " topol.tpr"
+.B Input, Opt.
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
+
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
+.BI "-od" " mindist.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-on" " numcont.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-o" " atm-pair.out"
+.B Output
+ Generic output file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " -1"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " -1"
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " -1"
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-[no]w" " no"
+ View output xvg, xpm, eps and pdb files
+
+.BI "-[no]matrix" " no"
+ Calculate half a matrix of group-group distances
+
+.BI "-d" " real" " 0.6"
+ Distance for contacts
+
+.BI "-[no]pi" " no"
+ Calculate minimum distance with periodic images
+
--- /dev/null
+.TH g_morph 1 "Tue 15 May 2001"
+.SH NAME
+g_morph
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3g_morph\fP
+.BI "-f1" " conf1.gro "
+.BI "-f2" " conf2.gro "
+.BI "-o" " interm.xtc "
+.BI "-or" " rms-interm.xvg "
+.BI "-n" " index.ndx "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-[no]w" ""
+.BI "-ninterm" " int "
+.BI "-first" " real "
+.BI "-last" " real "
+.BI "-[no]fit" ""
+.SH DESCRIPTION
+g_morph does a linear interpolation of conformations in order to
+create intermediates. Of course these are completely unphysical, but
+that you may try to justify yourself. Output is in the form of a
+generic trajectory. The number of intermediates can be controlled with
+the -ninterm flag. The first and last flag correspond to the way of
+interpolating: 0 corresponds to input structure 1 while
+1 corresponds to input strucutre 2.
+If you specify first 0 or last 1 extrapolation will be
+on the path from input structure x1 to x2. In general the coordinates
+of the intermediate x(i) out of N total intermidates correspond to:
+
+
+x(i) = x1 + (first+(i/(N-1))*(last-first))*(x2-x1)
+
+
+Finally the RMSD with respect to both input structures can be computed
+if explicitly selected (-or option). In that case an index file may be
+read to select what group RMS is computed from.
+.SH FILES
+.BI "-f1" " conf1.gro"
+.B Input
+ Generic structure: gro g96 pdb tpr tpb tpa
+
+.BI "-f2" " conf2.gro"
+.B Input
+ Generic structure: gro g96 pdb tpr tpb tpa
+
+.BI "-o" " interm.xtc"
+.B Output
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-or" " rms-interm.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 0"
+ Set the nicelevel
+
+.BI "-[no]w" " no"
+ View output xvg, xpm, eps and pdb files
+
+.BI "-ninterm" " int" " 11"
+ Number of intermediates
+
+.BI "-first" " real" " 0"
+ Corresponds to first generated structure (0 is input x0, see above)
+
+.BI "-last" " real" " 1"
+ Corresponds to last generated structure (1 is input x1, see above)
+
+.BI "-[no]fit" " yes"
+ Do a least squares fit of the second to the first structure before interpolating
+
--- /dev/null
+.TH g_msd 1 "Tue 15 May 2001"
+.SH NAME
+g_msd
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3g_msd\fP
+.BI "-f" " traj.xtc "
+.BI "-s" " topol.tpr "
+.BI "-n" " index.ndx "
+.BI "-o" " msd.xvg "
+.BI "-mol" " diff_mol.xvg "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-tu" " enum "
+.BI "-[no]w" ""
+.BI "-type" " enum "
+.BI "-lateral" " enum "
+.BI "-ngroup" " int "
+.BI "-[no]mw" ""
+.BI "-trestart" " time "
+.BI "-beginfit" " time "
+.BI "-endfit" " time "
+.SH DESCRIPTION
+g_msd computes the mean square displacement (MSD) of atoms from
+their initial positions. This provides an easy way to compute
+the diffusion constant using the Einstein relation.
+The diffusion constant is calculated by least squares fitting a
+straight line through the MSD from
+.B -beginfit
+to
+
+.B -endfit
+. An error estimate given, which is the difference
+of the diffusion coefficients obtained from fits over the two halfs
+of the fit interval.
+
+
+Option
+.B -mol
+plots the MSD for molecules, this implies
+
+.B -mw
+, i.e. for each inidividual molecule an diffusion constant
+is computed. When using an index file, it should contain molecule
+numbers instead of atom numbers.
+Using this option one also gets an accurate error estimate
+based on the statistics between individual molecules. Since one usually
+is interested in self-diffusion at infinite dilution this is probably
+the most useful number.
+
+
+.SH FILES
+.BI "-f" " traj.xtc"
+.B Input
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-s" " topol.tpr"
+.B Input
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
+
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
+.BI "-o" " msd.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-mol" " diff_mol.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " -1"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " -1"
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " -1"
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-tu" " enum" " ps"
+ Time unit: ps, fs, ns, us, ms, s, m or h
+
+.BI "-[no]w" " no"
+ View output xvg, xpm, eps and pdb files
+
+.BI "-type" " enum" " no"
+ Compute diffusion coefficient in one direction: no, x, y or z
+
+.BI "-lateral" " enum" " no"
+ Calculate the lateral diffusion in a plane perpendicular to: no, x, y or z
+
+.BI "-ngroup" " int" " 1"
+ Number of groups to calculate MSD for
+
+.BI "-[no]mw" " yes"
+ Mass weighted MSD
+
+.BI "-trestart" " time" " 0"
+ Time between restarting points in trajectory (ps)
+
+.BI "-beginfit" " time" " 0"
+ Start time for fitting the MSD (ps)
+
+.BI "-endfit" " time" " -1"
+ End time for fitting the MSD (ps), -1 is till end
+
--- /dev/null
+.TH g_nmeig 1 "Tue 15 May 2001"
+.SH NAME
+g_nmeig
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3g_nmeig\fP
+.BI "-f" " hessian.mtx "
+.BI "-s" " topol.tpr "
+.BI "-o" " eigenval.xvg "
+.BI "-v" " eigenvec.trr "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-[no]m" ""
+.BI "-first" " int "
+.BI "-last" " int "
+.SH DESCRIPTION
+g_nmeig calculates the eigenvectors/values of a (Hessian) matrix,
+which can be calculated with
+.B nmrun
+.
+The eigenvectors are written to a trajectory file (
+.B -v
+).
+The structure is written first with t=0. The eigenvectors
+are written as frames with the eigenvector number as timestamp.
+The eigenvectors can be analyzed with
+.B g_anaeig
+.
+An ensemble of structures can be generated from the eigenvectors with
+
+.B g_nmens
+.
+.SH FILES
+.BI "-f" " hessian.mtx"
+.B Input
+ Hessian matrix
+
+.BI "-s" " topol.tpr"
+.B Input
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
+
+.BI "-o" " eigenval.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-v" " eigenvec.trr"
+.B Output
+ Full precision trajectory: trr trj
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-[no]m" " yes"
+ Divide elements of Hessian by product of sqrt(mass) of involved atoms prior to diagonalization. This should be used for 'Normal Modes' analysis
+
+.BI "-first" " int" " 1"
+ First eigenvector to write away
+
+.BI "-last" " int" " 100"
+ Last eigenvector to write away
+
--- /dev/null
+.TH g_nmens 1 "Tue 15 May 2001"
+.SH NAME
+g_nmens
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3g_nmens\fP
+.BI "-v" " eigenvec.trr "
+.BI "-e" " eigenval.xvg "
+.BI "-s" " topol.tpr "
+.BI "-n" " index.ndx "
+.BI "-o" " ensemble.xtc "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-temp" " real "
+.BI "-seed" " int "
+.BI "-num" " int "
+.BI "-first" " int "
+.BI "-last" " int "
+.SH DESCRIPTION
+
+.B g_nmens
+generates an ensemble around an average structure
+in a subspace which is defined by a set of normal modes (eigenvectors).
+The eigenvectors are assumed to be mass-weighted.
+The position along each eigenvector is randomly taken from a Gaussian
+distribution with variance kT/eigenvalue.
+
+
+By default the starting eigenvector is set to 7, since the first six
+normal modes are the translational and rotational degrees of freedom.
+.SH FILES
+.BI "-v" " eigenvec.trr"
+.B Input
+ Full precision trajectory: trr trj
+
+.BI "-e" " eigenval.xvg"
+.B Input
+ xvgr/xmgr file
+
+.BI "-s" " topol.tpr"
+.B Input
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
+
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
+.BI "-o" " ensemble.xtc"
+.B Output
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-temp" " real" " 300"
+ Temperature in Kelvin
+
+.BI "-seed" " int" " -1"
+ Random seed, -1 generates a seed from time and pid
+
+.BI "-num" " int" " 100"
+ Number of structures to generate
+
+.BI "-first" " int" " 7"
+ First eigenvector to use (-1 is select)
+
+.BI "-last" " int" " -1"
+ Last eigenvector to use (-1 is till the last)
+
--- /dev/null
+.TH g_order 1 "Tue 15 May 2001"
+.SH NAME
+g_order
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3g_order\fP
+.BI "-f" " traj.xtc "
+.BI "-n" " index.ndx "
+.BI "-s" " topol.tpr "
+.BI "-o" " order.xvg "
+.BI "-od" " deuter.xvg "
+.BI "-os" " sliced.xvg "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-[no]w" ""
+.BI "-d" " enum "
+.BI "-sl" " int "
+.BI "-[no]szonly" ""
+.BI "-[no]unsat" ""
+.SH DESCRIPTION
+Compute the order parameter per atom for carbon tails. For atom i the
+vector i-1, i+1 is used together with an axis. The index file has to contain
+a group with all equivalent atoms in all tails for each atom the
+order parameter has to be calculated for. The program can also give all
+diagonal elements of the order tensor and even calculate the deuterium
+order parameter Scd (default). If the option -szonly is given, only one
+order tensor component (specified by the -d option) is given and the
+order parameter per slice is calculated as well. If -szonly is not
+selected, all diagonal elements and the deuterium order parameter is
+given.
+.SH FILES
+.BI "-f" " traj.xtc"
+.B Input
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-n" " index.ndx"
+.B Input
+ Index file
+
+.BI "-s" " topol.tpr"
+.B Input
+ Generic run input: tpr tpb tpa
+
+.BI "-o" " order.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-od" " deuter.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-os" " sliced.xvg"
+.B Output
+ xvgr/xmgr file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " -1"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " -1"
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " -1"
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-[no]w" " no"
+ View output xvg, xpm, eps and pdb files
+
+.BI "-d" " enum" " z"
+ Direction of the normal on the membrane: z, x or y
+
+.BI "-sl" " int" " 1"
+ Calculate order parameter as function of boxlength, dividing the box in nr slices.
+
+.BI "-[no]szonly" " no"
+ Only give Sz element of order tensor. (axis can be specified with -d)
+
+.BI "-[no]unsat" " no"
+ Calculate order parameters for unsaturated carbons. Note that this cannot be mixed with normal order parameters.
+
--- /dev/null
+.TH g_potential 1 "Tue 15 May 2001"
+.SH NAME
+g_potential
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3g_potential\fP
+.BI "-f" " traj.xtc "
+.BI "-n" " index.ndx "
+.BI "-s" " topol.tpr "
+.BI "-o" " potential.xvg "
+.BI "-oc" " charge.xvg "
+.BI "-of" " field.xvg "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-[no]w" ""
+.BI "-d" " string "
+.BI "-sl" " int "
+.BI "-cb" " int "
+.BI "-ce" " int "
+.BI "-tz" " real "
+.BI "-[no]spherical" ""
+.SH DESCRIPTION
+Compute the electrostatical potential across the box. The potential iscalculated by first summing the charges per slice and then integratingtwice of this charge distribution. Periodic boundaries are not taken into account. Reference of potential is taken to be the left side ofthe box. It's also possible to calculate the potential in sphericalcoordinates as function of r by calculating a charge distribution inspherical slices and twice integrating them. epsilon_r is taken as 1,2 is more appropriate in many cases
+.SH FILES
+.BI "-f" " traj.xtc"
+.B Input
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-n" " index.ndx"
+.B Input
+ Index file
+
+.BI "-s" " topol.tpr"
+.B Input
+ Generic run input: tpr tpb tpa
+
+.BI "-o" " potential.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-oc" " charge.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-of" " field.xvg"
+.B Output
+ xvgr/xmgr file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " -1"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " -1"
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " -1"
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-[no]w" " no"
+ View output xvg, xpm, eps and pdb files
+
+.BI "-d" " string" " Z"
+ Take the normal on the membrane in direction X, Y or Z.
+
+.BI "-sl" " int" " 10"
+ Calculate potential as function of boxlength, dividing the box in nr slices.
+
+.BI "-cb" " int" " 0"
+ Discard first nr slices of box for integration
+
+.BI "-ce" " int" " 0"
+ Discard last nr slices of box for integration
+
+.BI "-tz" " real" " 0"
+ Translate all coordinates distance in the direction of the box
+
+.BI "-[no]spherical" " no"
+ Calculate spherical thingie
+
+.SH DIAGNOSTICS
+\- Discarding slices for integration should not be necessary.
+
--- /dev/null
+.TH g_rama 1 "Tue 15 May 2001"
+.SH NAME
+g_rama
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3g_rama\fP
+.BI "-f" " traj.xtc "
+.BI "-s" " topol.tpr "
+.BI "-o" " rama.xvg "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-[no]w" ""
+.SH DESCRIPTION
+g_rama selects the Phi/Psi dihedral combinations from your topology file
+and computes these as a function of time.
+Using simple Unix tools such as
+.I grep
+you can select out
+specific residues.
+.SH FILES
+.BI "-f" " traj.xtc"
+.B Input
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-s" " topol.tpr"
+.B Input
+ Generic run input: tpr tpb tpa
+
+.BI "-o" " rama.xvg"
+.B Output
+ xvgr/xmgr file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " -1"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " -1"
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " -1"
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-[no]w" " no"
+ View output xvg, xpm, eps and pdb files
+
--- /dev/null
+.TH g_rdf 1 "Tue 15 May 2001"
+.SH NAME
+g_rdf
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3g_rdf\fP
+.BI "-f" " traj.xtc "
+.BI "-s" " topol.tpr "
+.BI "-n" " index.ndx "
+.BI "-o" " rdf.xvg "
+.BI "-sq" " sq.xvg "
+.BI "-cn" " rdf_cn.xvg "
+.BI "-hq" " hq.xvg "
+.BI "-image" " sq.xpm "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-[no]w" ""
+.BI "-bin" " real "
+.BI "-[no]com" ""
+.BI "-cut" " real "
+.BI "-fade" " real "
+.BI "-grid" " real "
+.BI "-nlevel" " int "
+.BI "-wave" " real "
+.SH DESCRIPTION
+The structure of liquids can be studied by either neutron or X-ray
+scattering. The most common way to describe liquid structure is by a
+radial distribution function. However, this is not easy to obtain from
+a scattering experiment.
+
+
+g_rdf calculates radial distribution functions in different ways.
+The normal method is around a (set of) particle(s), the other method
+is around the center of mass of a set of particles.
+
+
+If a run input file is supplied (
+.B -s
+), exclusions defined
+in that file are taken into account when calculating the rdf.
+The option
+.B -cut
+is meant as an alternative way to avoid
+intramolecular peaks in the rdf plot.
+It is however better to supply a run input file with a higher number of
+exclusions. For eg. benzene a topology with nrexcl set to 5
+would eliminate all intramolecular contributions to the rdf.
+Note that all atoms in the selected groups are used, also the ones
+that don't have Lennard-Jones interactions.
+
+
+Option
+.B -cn
+produces the cumulative number rdf.
+
+To bridge the gap between theory and experiment structure factors can
+be computed (option
+.B -sq
+). The algorithm uses FFT, the gridspacing of which is determined by option
+.B -grid
+.
+.SH FILES
+.BI "-f" " traj.xtc"
+.B Input
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-s" " topol.tpr"
+.B Input, Opt.
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
+
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
+.BI "-o" " rdf.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-sq" " sq.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-cn" " rdf_cn.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-hq" " hq.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-image" " sq.xpm"
+.B Output, Opt.
+ X PixMap compatible matrix file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " -1"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " -1"
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " -1"
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-[no]w" " no"
+ View output xvg, xpm, eps and pdb files
+
+.BI "-bin" " real" " 0.001"
+ Binwidth (nm)
+
+.BI "-[no]com" " no"
+ RDF with respect to the center of mass of first group
+
+.BI "-cut" " real" " 0"
+ Shortest distance (nm) to be considered
+
+.BI "-fade" " real" " 0"
+ From this distance onwards the RDF is tranformed by g'(r) = 1 + [g(r)-1] exp(-(r/fade-1)2 to make it go to 1 smoothly. If fade is 0.0 nothing is done.
+
+.BI "-grid" " real" " 0.05"
+ Grid spacing (in nm) for FFTs when computing structure factors
+
+.BI "-nlevel" " int" " 20"
+ Number of different colors in the diffraction image
+
+.BI "-wave" " real" " 0.1"
+ Wavelength for X-rays/Neutrons for scattering. 0.1 nm corresponds to roughly 12 keV
+
--- /dev/null
+.TH g_rms 1 "Tue 15 May 2001"
+.SH NAME
+g_rms
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3g_rms\fP
+.BI "-s" " topol.tpr "
+.BI "-f" " traj.xtc "
+.BI "-f2" " traj.xtc "
+.BI "-n" " index.ndx "
+.BI "-o" " rmsd.xvg "
+.BI "-mir" " rmsdmir.xvg "
+.BI "-a" " avgrp.xvg "
+.BI "-dist" " rmsd-dist.xvg "
+.BI "-m" " rmsd.xpm "
+.BI "-bin" " rmsd.dat "
+.BI "-bm" " bond.xpm "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-tu" " enum "
+.BI "-[no]w" ""
+.BI "-what" " enum "
+.BI "-[no]pbc" ""
+.BI "-[no]fit" ""
+.BI "-prev" " int "
+.BI "-[no]split" ""
+.BI "-skip" " int "
+.BI "-skip2" " int "
+.BI "-max" " real "
+.BI "-min" " real "
+.BI "-bmax" " real "
+.BI "-bmin" " real "
+.BI "-nlevels" " int "
+.SH DESCRIPTION
+g_rms compares two structures by computing the root mean square
+deviation (RMSD), the size-independent 'rho' similarity parameter
+(rho) or the scaled rho (rhosc),
+reference Maiorov & Crippen, PROTEINS 22, 273 (1995).
+This is selected by
+.B -what
+.
+
+Each structure from a trajectory (
+.B -f
+) is compared to a
+reference structure from a run input file by least-squares fitting
+the structures on top of each other. The reference structure is taken
+from the structure file (
+.B -s
+).
+
+
+With option
+.B -mir
+also a comparison with the mirror image of
+the reference structure is calculated.
+
+
+Option
+.B -prev
+produces the comparison with a previous frame.
+
+
+Option
+.B -m
+produces a matrix in
+.B .xpm
+format of
+comparison values of each structure in the trajectory with respect to
+each other structure. This file can be visualized with for instance
+
+.B xv
+and can be converted to postscript with
+.B xpm2ps
+.
+
+
+All the structures are fitted pairwise.
+
+
+With
+.B -f2
+, the 'other structures' are taken from a second
+trajectory.
+
+
+Option
+.B -bin
+does a binary dump of the comparison matrix.
+
+
+Option
+.B -bm
+produces a matrix of average bond angle deviations
+analogously to the
+.B -m
+option. Only bonds between atoms in the
+comparison group are considered.
+.SH FILES
+.BI "-s" " topol.tpr"
+.B Input
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
+
+.BI "-f" " traj.xtc"
+.B Input
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-f2" " traj.xtc"
+.B Input, Opt.
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
+.BI "-o" " rmsd.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-mir" " rmsdmir.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-a" " avgrp.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-dist" " rmsd-dist.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-m" " rmsd.xpm"
+.B Output, Opt.
+ X PixMap compatible matrix file
+
+.BI "-bin" " rmsd.dat"
+.B Output, Opt.
+ Generic data file
+
+.BI "-bm" " bond.xpm"
+.B Output, Opt.
+ X PixMap compatible matrix file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " -1"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " -1"
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " -1"
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-tu" " enum" " ps"
+ Time unit: ps, fs, ns, us, ms, s, m or h
+
+.BI "-[no]w" " no"
+ View output xvg, xpm, eps and pdb files
+
+.BI "-what" " enum" " rmsd"
+ Structural difference measure: rmsd, rho or rhosc
+
+.BI "-[no]pbc" " yes"
+ PBC check
+
+.BI "-[no]fit" " yes"
+ Fit to reference structure
+
+.BI "-prev" " int" " 0"
+ Compare with previous frame
+
+.BI "-[no]split" " no"
+ Split graph where time is zero
+
+.BI "-skip" " int" " 1"
+ Only write every nr-th frame to matrix
+
+.BI "-skip2" " int" " 1"
+ Only write every nr-th frame to matrix
+
+.BI "-max" " real" " -1"
+ Maximum level in comparison matrix
+
+.BI "-min" " real" " -1"
+ Minimum level in comparison matrix
+
+.BI "-bmax" " real" " -1"
+ Maximum level in bond angle matrix
+
+.BI "-bmin" " real" " -1"
+ Minimum level in bond angle matrix
+
+.BI "-nlevels" " int" " 80"
+ Number of levels in the matrices
+
--- /dev/null
+.TH g_rmsdist 1 "Tue 15 May 2001"
+.SH NAME
+g_rmsdist
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3g_rmsdist\fP
+.BI "-f" " traj.xtc "
+.BI "-s" " topol.tpr "
+.BI "-n" " index.ndx "
+.BI "-equiv" " equiv.dat "
+.BI "-o" " distrmsd.xvg "
+.BI "-rms" " rmsdist.xpm "
+.BI "-scl" " rmsscale.xpm "
+.BI "-mean" " rmsmean.xpm "
+.BI "-nmr3" " nmr3.xpm "
+.BI "-nmr6" " nmr6.xpm "
+.BI "-noe" " noe.dat "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-[no]w" ""
+.BI "-nlevels" " int "
+.BI "-max" " real "
+.BI "-[no]sumh" ""
+.SH DESCRIPTION
+g_rmsdist computes the root mean square deviation of atom distances,
+which has the advantage that no fit is needed like in standard RMS
+deviation as computed by g_rms.
+The reference structure is taken from the structure file.
+The rmsd at time t is calculated as the rms
+of the differences in distance between atom-pairs in the reference
+structure and the structure at time t.
+
+
+g_rmsdist can also produce matrices of the rms distances, rms distances
+scaled with the mean distance and the mean distances and matrices with
+NMR averaged distances (1/r3 and 1/r6 averaging). Finally, lists
+of atom pairs with 1/r3 and 1/r6 averaged distance below the
+maximum distance (
+.B -max
+, which will default to 0.6 in this case)
+can be generated, by default averaging over equivalent hydrogens
+(all triplets of hydrogens named *[123]). Additionally a list of
+equivalent atoms can be supplied (
+.B -equiv
+), each line containing
+a set of equivalent atoms specified as residue number and name and
+atom name; e.g.:
+
+
+
+.B 3 SER HB1 3 SER HB2
+
+
+
+Residue and atom names must exactly match those in the structure
+file, including case. Specifying non-sequential atoms is undefined.
+.SH FILES
+.BI "-f" " traj.xtc"
+.B Input
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-s" " topol.tpr"
+.B Input
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
+
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
+.BI "-equiv" " equiv.dat"
+.B Input, Opt.
+ Generic data file
+
+.BI "-o" " distrmsd.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-rms" " rmsdist.xpm"
+.B Output, Opt.
+ X PixMap compatible matrix file
+
+.BI "-scl" " rmsscale.xpm"
+.B Output, Opt.
+ X PixMap compatible matrix file
+
+.BI "-mean" " rmsmean.xpm"
+.B Output, Opt.
+ X PixMap compatible matrix file
+
+.BI "-nmr3" " nmr3.xpm"
+.B Output, Opt.
+ X PixMap compatible matrix file
+
+.BI "-nmr6" " nmr6.xpm"
+.B Output, Opt.
+ X PixMap compatible matrix file
+
+.BI "-noe" " noe.dat"
+.B Output, Opt.
+ Generic data file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " -1"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " -1"
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " -1"
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-[no]w" " no"
+ View output xvg, xpm, eps and pdb files
+
+.BI "-nlevels" " int" " 40"
+ Discretize rms in levels
+
+.BI "-max" " real" " -1"
+ Maximum level in matrices
+
+.BI "-[no]sumh" " yes"
+ average distance over equivalent hydrogens
+
--- /dev/null
+.TH g_rmsf 1 "Tue 15 May 2001"
+.SH NAME
+g_rmsf
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3g_rmsf\fP
+.BI "-f" " traj.xtc "
+.BI "-s" " topol.tpr "
+.BI "-n" " index.ndx "
+.BI "-q" " eiwit.pdb "
+.BI "-oq" " bfac.pdb "
+.BI "-ox" " xaver.pdb "
+.BI "-o" " rmsf.xvg "
+.BI "-od" " rmsdev.xvg "
+.BI "-oc" " correl.xvg "
+.BI "-dir" " rmsf.log "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-[no]w" ""
+.BI "-[no]res" ""
+.BI "-[no]aniso" ""
+.SH DESCRIPTION
+g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard
+deviation) of atomic positions
+after first fitting to a reference frame.
+
+
+With option
+.B -oq
+the RMSF values are converted to B-factor
+values, which are written to a pdb file with the coordinates, of the
+structure file, or of a pdb file when
+.B -q
+is specified.
+Option
+.B -ox
+writes the B-factors to a file with the average
+coordinates.
+
+
+With the option
+.B -od
+the root mean square deviation with
+respect to the reference structure is calculated.
+
+
+With the option
+.B aniso
+g_rmsf will compute anisotropic
+temperature factors and then it will also output average coordinates
+and a pdb file with ANISOU records (corresonding to the
+.B -oq
+
+or
+.B -ox
+option). Please note that the U values
+are orientation dependent, so before comparison with experimental data
+you should verify that you fit to the experimental coordinates.
+
+
+When a pdb input file is passed to the program and the
+.B -aniso
+
+flag is set
+a correlation plot of the Uij will be created, if any anisotropic
+temperature factors are present in the pdb file.
+
+
+With option
+.B -dir
+the average MSF (3x3) matrix is diagonalized.
+This shows the directions in which the atoms fluctuate the most and
+the least.
+.SH FILES
+.BI "-f" " traj.xtc"
+.B Input
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-s" " topol.tpr"
+.B Input
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
+
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
+.BI "-q" " eiwit.pdb"
+.B Input, Opt.
+ Protein data bank file
+
+.BI "-oq" " bfac.pdb"
+.B Output, Opt.
+ Protein data bank file
+
+.BI "-ox" " xaver.pdb"
+.B Output, Opt.
+ Protein data bank file
+
+.BI "-o" " rmsf.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-od" " rmsdev.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-oc" " correl.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-dir" " rmsf.log"
+.B Output, Opt.
+ Log file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " -1"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " -1"
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " -1"
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-[no]w" " no"
+ View output xvg, xpm, eps and pdb files
+
+.BI "-[no]res" " no"
+ Calculate averages for each residue
+
+.BI "-[no]aniso" " no"
+ Compute anisotropic termperature factors
+
--- /dev/null
+.TH g_rotacf 1 "Tue 15 May 2001"
+.SH NAME
+g_rotacf
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3g_rotacf\fP
+.BI "-f" " traj.xtc "
+.BI "-s" " topol.tpr "
+.BI "-n" " index.ndx "
+.BI "-o" " rotacf.xvg "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-[no]w" ""
+.BI "-[no]d" ""
+.BI "-[no]aver" ""
+.BI "-acflen" " int "
+.BI "-[no]normalize" ""
+.BI "-P" " enum "
+.BI "-fitfn" " enum "
+.BI "-ncskip" " int "
+.BI "-beginfit" " real "
+.BI "-endfit" " real "
+.SH DESCRIPTION
+g_rotacf calculates the rotational correlation function
+for molecules. Three atoms (i,j,k) must be given in the index
+file, defining two vectors ij and jk. The rotational acf
+is calculated as the autocorrelation function of the vector
+n = ij x jk, i.e. the cross product of the two vectors.
+Since three atoms span a plane, the order of the three atoms
+does not matter. Optionally, controlled by the -d switch, you can
+calculate the rotational correlation function for linear molecules
+by specifying two atoms (i,j) in the index file.
+
+
+
+EXAMPLES
+
+
+g_rotacf -P 1 -nparm 2 -fft -n index -o rotacf-x-P1
+-fa expfit-x-P1 -beginfit 2.5 -endfit 20.0
+
+
+This will calculate the rotational correlation function using a first
+order Legendre polynomial of the angle of a vector defined by the index
+file. The correlation function will be fitted from 2.5 ps till 20.0 ps
+to a two parameter exponential
+
+.SH FILES
+.BI "-f" " traj.xtc"
+.B Input
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-s" " topol.tpr"
+.B Input
+ Generic run input: tpr tpb tpa
+
+.BI "-n" " index.ndx"
+.B Input
+ Index file
+
+.BI "-o" " rotacf.xvg"
+.B Output
+ xvgr/xmgr file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " -1"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " -1"
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " -1"
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-[no]w" " no"
+ View output xvg, xpm, eps and pdb files
+
+.BI "-[no]d" " no"
+ Use index doublets (vectors) for correlation function instead of triplets (planes)
+
+.BI "-[no]aver" " yes"
+ Average over molecules
+
+.BI "-acflen" " int" " -1"
+ Length of the ACF, default is half the number of frames
+
+.BI "-[no]normalize" " yes"
+ Normalize ACF
+
+.BI "-P" " enum" " 0"
+ Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or 3
+
+.BI "-fitfn" " enum" " none"
+ Fit function: none, exp, aexp, exp_exp or vac
+
+.BI "-ncskip" " int" " 0"
+ Skip N points in the output file of correlation functions
+
+.BI "-beginfit" " real" " 0"
+ Time where to begin the exponential fit of the correlation function
+
+.BI "-endfit" " real" " -1"
+ Time where to end the exponential fit of the correlation function, -1 is till the end
+
--- /dev/null
+.TH g_saltbr 1 "Tue 15 May 2001"
+.SH NAME
+g_saltbr
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3g_saltbr\fP
+.BI "-f" " traj.xtc "
+.BI "-s" " topol.tpr "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-t" " real "
+.BI "-[no]sep" ""
+.SH DESCRIPTION
+g_saltbr plots the difference between all combination of charged groups
+as a function of time. The groups are combined in different ways.A minimum distance can be given, (eg. the cut-off), then groups
+that are never closer than that distance will not be plotted.
+
+Output will be in a number of fixed filenames, min-min.xvg,min-plus.xvg
+and plus-plus.xvg, or files for every individual ion-pair if selected
+.SH FILES
+.BI "-f" " traj.xtc"
+.B Input
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-s" " topol.tpr"
+.B Input
+ Generic run input: tpr tpb tpa
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " -1"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " -1"
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " -1"
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-t" " real" " 1000"
+ trunc distance
+
+.BI "-[no]sep" " no"
+ Use separate files for each interaction (may be MANY)
+
--- /dev/null
+.TH g_sas 1 "Tue 15 May 2001"
+.SH NAME
+g_sas
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3g_sas\fP
+.BI "-f" " traj.xtc "
+.BI "-s" " topol.tpr "
+.BI "-o" " area.xvg "
+.BI "-r" " resarea.xvg "
+.BI "-q" " connelly.pdb "
+.BI "-ao" " atomarea.xvg "
+.BI "-n" " index.ndx "
+.BI "-i" " surfat.itp "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-[no]w" ""
+.BI "-solsize" " real "
+.BI "-ndots" " int "
+.BI "-qmax" " real "
+.BI "-minarea" " real "
+.BI "-skip" " int "
+.BI "-[no]prot" ""
+.SH DESCRIPTION
+g_sas computes hydrophobic and total solvent accessible surface area.
+As a side effect the Connolly surface can be generated as well in
+a pdb file where the nodes are represented as atoms and the vertices
+connecting the nearest nodes as CONECT records. The area can be plotted
+per atom and per residue as well (option -ao). In combination with
+the latter option an
+.B itp
+file can be generated (option -i)
+which can be used to restrain surface atoms.
+.SH FILES
+.BI "-f" " traj.xtc"
+.B Input
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-s" " topol.tpr"
+.B Input
+ Generic run input: tpr tpb tpa
+
+.BI "-o" " area.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-r" " resarea.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-q" " connelly.pdb"
+.B Output, Opt.
+ Protein data bank file
+
+.BI "-ao" " atomarea.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
+.BI "-i" " surfat.itp"
+.B Output, Opt.
+ Include file for topology
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " -1"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " -1"
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " -1"
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-[no]w" " no"
+ View output xvg, xpm, eps and pdb files
+
+.BI "-solsize" " real" " 0.14"
+ Radius of the solvent probe (nm)
+
+.BI "-ndots" " int" " 24"
+ Number of dots per sphere, more dots means more accuracy
+
+.BI "-qmax" " real" " 0.2"
+ The maximum charge (e, absolute value) of a hydrophobic atom
+
+.BI "-minarea" " real" " 0.5"
+ The maximum charge (e, absolute value) of a hydrophobic atom
+
+.BI "-skip" " int" " 1"
+ Do only every nth frame
+
+.BI "-[no]prot" " yes"
+ Output the protein to the connelly pdb file too
+
--- /dev/null
+.TH g_sgangle 1 "Tue 15 May 2001"
+.SH NAME
+g_sgangle
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3g_sgangle\fP
+.BI "-f" " traj.xtc "
+.BI "-n" " index.ndx "
+.BI "-s" " topol.tpr "
+.BI "-oa" " sg_angle.xvg "
+.BI "-od" " sg_dist.xvg "
+.BI "-od1" " sg_dist1.xvg "
+.BI "-od2" " sg_dist2.xvg "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-[no]w" ""
+.SH DESCRIPTION
+Compute the angle and distance between two groups.
+The groups are defined by a number of atoms given in an index file and
+may be two or three atoms in size.
+The angles calculated depend on the order in which the atoms are
+given. Giving for instance 5 6 will rotate the vector 5-6 with
+180 degrees compared to giving 6 5.
+
+If three atoms are given,
+the normal on the plane spanned by those three atoms will be
+calculated, using the formula P1P2 x P1P3.
+The cos of the angle is calculated, using the inproduct of the two
+normalized vectors.
+
+
+Here is what some of the file options do:
+
+-oa: Angle between the two groups specified in the index file. If a group contains three atoms the normal to the plane defined by those three atoms will be used. If a group contains two atoms, the vector defined by those two atoms will be used.
+
+-od: Distance between two groups. Distance is taken from the center of one group to the center of the other group.
+
+-od1: If one plane and one vector is given, the distances for each of the atoms from the center of the plane is given seperately.
+
+-od2: For two planes this option has no meaning.
+.SH FILES
+.BI "-f" " traj.xtc"
+.B Input
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-n" " index.ndx"
+.B Input
+ Index file
+
+.BI "-s" " topol.tpr"
+.B Input
+ Generic run input: tpr tpb tpa
+
+.BI "-oa" " sg_angle.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-od" " sg_dist.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-od1" " sg_dist1.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-od2" " sg_dist2.xvg"
+.B Output
+ xvgr/xmgr file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " -1"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " -1"
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " -1"
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-[no]w" " no"
+ View output xvg, xpm, eps and pdb files
+
--- /dev/null
+.TH g_sorient 1 "Tue 15 May 2001"
+.SH NAME
+g_sorient
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3g_sorient\fP
+.BI "-f" " traj.xtc "
+.BI "-s" " topol.tpr "
+.BI "-n" " index.ndx "
+.BI "-o" " sori.xvg "
+.BI "-no" " snor.xvg "
+.BI "-ro" " sord.xvg "
+.BI "-co" " scum.xvg "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-[no]w" ""
+.BI "-[no]com" ""
+.BI "-rmin" " real "
+.BI "-rmax" " real "
+.BI "-nbin" " int "
+.SH DESCRIPTION
+g_sorient analyzes solvent orientation around solutes.
+It calculates two angles between the vector from one or more
+reference positions to the first atom of each solvent molecule:
+theta1: the angle with the vector from the first atom of the solvent
+molecule to the midpoint between atoms 2 and 3.
+
+theta2: the angle with the normal of the solvent plane, defined by the
+same three atoms.
+
+The reference can be a set of atoms or
+the center of mass of a set of atoms. The group of solvent atoms should
+consist of 3 atoms per solvent molecule.
+Only solvent molecules between
+.B -rmin
+and
+.B -rmax
+are
+considered each frame.
+
+
+
+.B -o
+: angle distribution of theta1.
+
+
+
+.B -no
+: angle distribution of theta2.
+
+
+
+.B -ro
+: cos(theta1) and 3cos2(theta2)-1 as a function of the
+distance.
+
+
+
+.B -ro
+: the sum over all solvent molecules within distance r
+of cos(theta1) and 3cos2(theta2)-1 as a function of r.
+
+
+.SH FILES
+.BI "-f" " traj.xtc"
+.B Input
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-s" " topol.tpr"
+.B Input
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
+
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
+.BI "-o" " sori.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-no" " snor.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-ro" " sord.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-co" " scum.xvg"
+.B Output
+ xvgr/xmgr file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " -1"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " -1"
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " -1"
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-[no]w" " no"
+ View output xvg, xpm, eps and pdb files
+
+.BI "-[no]com" " no"
+ Use the center of mass as the reference postion
+
+.BI "-rmin" " real" " 0"
+ Minimum distance
+
+.BI "-rmax" " real" " 0.5"
+ Maximum distance
+
+.BI "-nbin" " int" " 20"
+ Number of bins
+
--- /dev/null
+.TH g_tcaf 1 "Tue 15 May 2001"
+.SH NAME
+g_tcaf
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3g_tcaf\fP
+.BI "-f" " traj.trr "
+.BI "-s" " topol.tpr "
+.BI "-n" " index.ndx "
+.BI "-ot" " transcur.xvg "
+.BI "-oa" " tcaf_all.xvg "
+.BI "-o" " tcaf.xvg "
+.BI "-of" " tcaf_fit.xvg "
+.BI "-oc" " tcaf_cub.xvg "
+.BI "-ov" " visc_k.xvg "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-[no]w" ""
+.BI "-[no]mol" ""
+.BI "-[no]k34" ""
+.BI "-wt" " real "
+.SH DESCRIPTION
+g_tcaf computes tranverse current autocorrelations.
+These are used to estimate the shear viscosity eta.
+For details see: Palmer, JCP 49 (1994) pp 359-366.
+
+
+Transverse currents are calculated using the
+k-vectors (1,0,0) and (2,0,0) each also in the y- and z-direction,
+(1,1,0) and (1,-1,0) each also in the 2 other plains (these vectors
+are not independent) and (1,1,1) and the 3 other box diagonals (also
+not independent). For each k-vector the sine and cosine are used, in
+combination with the velocity in 2 perpendicular directions. This gives
+a total of 16*2*2=64 transverse currents. One autocorrelation is
+calculated fitted for each k-vector, which gives 16 tcaf's. Each of
+these tcaf's is fitted to f(t) = exp(-v)(cosh(Wv) + 1/W sinh(Wv)),
+v = -t/(2 tau), W = sqrt(1 - 4 tau eta/rho k2), which gives 16 tau's
+and eta's. The fit weights decay with time as exp(-t/wt), the tcaf and
+fit are calculated up to time 5*wt.
+The eta's should be fitted to 1 - a eta(k) k2, from which
+one can estimate the shear viscosity at k=0.
+
+
+When the box is cubic, one can use the option
+.B -oc
+, which
+averages the tcaf's over all k-vectors with the same length.
+This results in more accurate tcaf's.
+Both the cubic tcaf's and fits are written to
+.B -oc
+
+The cubic eta estimates are also written to
+.B -ov
+.
+
+
+With option
+.B -mol
+the transverse current is determined of
+molecules instead of atoms. In this case the index group should
+consist of molecule numbers instead of atom numbers.
+
+
+The k-dependent viscosities in the
+.B -ov
+file should be
+fitted to eta(k) = eta0 (1 - a k2) to obtain the viscosity at
+infinite wavelength.
+
+
+NOTE: make sure you write coordinates and velocities often enough.
+The initial, non-exponential, part of the autocorrelation function
+is very important for obtaining a good fit.
+.SH FILES
+.BI "-f" " traj.trr"
+.B Input
+ Full precision trajectory: trr trj
+
+.BI "-s" " topol.tpr"
+.B Input, Opt.
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
+
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
+.BI "-ot" " transcur.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-oa" " tcaf_all.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-o" " tcaf.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-of" " tcaf_fit.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-oc" " tcaf_cub.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-ov" " visc_k.xvg"
+.B Output
+ xvgr/xmgr file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " -1"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " -1"
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " -1"
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-[no]w" " no"
+ View output xvg, xpm, eps and pdb files
+
+.BI "-[no]mol" " no"
+ Calculate tcaf of molecules
+
+.BI "-[no]k34" " no"
+ Also use k=(3,0,0) and k=(4,0,0)
+
+.BI "-wt" " real" " 5"
+ Exponential decay time for the TCAF fit weights
+
--- /dev/null
+.TH g_traj 1 "Tue 15 May 2001"
+.SH NAME
+g_traj
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3g_traj\fP
+.BI "-f" " traj.xtc "
+.BI "-s" " topol.tpr "
+.BI "-n" " index.ndx "
+.BI "-ox" " coord.xvg "
+.BI "-ov" " veloc.xvg "
+.BI "-of" " force.xvg "
+.BI "-ob" " box.xvg "
+.BI "-ot" " temp.xvg "
+.BI "-ekr" " ekrot.xvg "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-[no]w" ""
+.BI "-[no]com" ""
+.BI "-[no]mol" ""
+.BI "-[no]nojump" ""
+.BI "-[no]x" ""
+.BI "-[no]y" ""
+.BI "-[no]z" ""
+.BI "-[no]len" ""
+.SH DESCRIPTION
+g_traj plots coordinates, velocities, forces and/or the box.
+With
+.B -com
+the coordinates, velocities and forces are
+calculated for the center of mass of each group.
+When
+.B -mol
+is set, the numbers in the index file are
+interpreted as molecule numbers and the same procedure as with
+
+.B -com
+is used for each molecule.
+
+
+Option
+.B -ot
+plots the temperature of each group.
+This implies
+.B -com
+.
+
+
+Option
+.B -ekr
+plots the rotational kinetic energy of each group.
+This implies
+.B -com
+.
+.SH FILES
+.BI "-f" " traj.xtc"
+.B Input
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-s" " topol.tpr"
+.B Input
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
+
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
+.BI "-ox" " coord.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-ov" " veloc.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-of" " force.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-ob" " box.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-ot" " temp.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-ekr" " ekrot.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " -1"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " -1"
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " -1"
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-[no]w" " no"
+ View output xvg, xpm, eps and pdb files
+
+.BI "-[no]com" " no"
+ Plot data for the com of each group
+
+.BI "-[no]mol" " no"
+ Index contains molecule numbers iso atom numbers
+
+.BI "-[no]nojump" " no"
+ Remove jumps of atoms across the box
+
+.BI "-[no]x" " yes"
+ Plot X-component
+
+.BI "-[no]y" " yes"
+ Plot Y-component
+
+.BI "-[no]z" " yes"
+ Plot Z-component
+
+.BI "-[no]len" " no"
+ Plot vector length
+
--- /dev/null
+.TH g_velacc 1 "Tue 15 May 2001"
+.SH NAME
+g_velacc
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3g_velacc\fP
+.BI "-f" " traj.trr "
+.BI "-s" " topol.tpr "
+.BI "-n" " index.ndx "
+.BI "-o" " vac.xvg "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-[no]w" ""
+.BI "-[no]mol" ""
+.BI "-acflen" " int "
+.BI "-[no]normalize" ""
+.BI "-P" " enum "
+.BI "-fitfn" " enum "
+.BI "-ncskip" " int "
+.BI "-beginfit" " real "
+.BI "-endfit" " real "
+.SH DESCRIPTION
+g_velacc computes the velocity autocorrelation function.
+When the
+.B -s
+option is used, the momentum autocorrelation
+function is calculated.
+
+
+With option
+.B -mol
+the momentum autocorrelation function of
+molecules is calculated. In this case the index group should consist
+of molecule numbers instead of atom numbers.
+.SH FILES
+.BI "-f" " traj.trr"
+.B Input
+ Full precision trajectory: trr trj
+
+.BI "-s" " topol.tpr"
+.B Input, Opt.
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
+
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
+.BI "-o" " vac.xvg"
+.B Output
+ xvgr/xmgr file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " -1"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " -1"
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " -1"
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-[no]w" " no"
+ View output xvg, xpm, eps and pdb files
+
+.BI "-[no]mol" " no"
+ Calculate vac of molecules
+
+.BI "-acflen" " int" " -1"
+ Length of the ACF, default is half the number of frames
+
+.BI "-[no]normalize" " yes"
+ Normalize ACF
+
+.BI "-P" " enum" " 0"
+ Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or 3
+
+.BI "-fitfn" " enum" " none"
+ Fit function: none, exp, aexp, exp_exp or vac
+
+.BI "-ncskip" " int" " 0"
+ Skip N points in the output file of correlation functions
+
+.BI "-beginfit" " real" " 0"
+ Time where to begin the exponential fit of the correlation function
+
+.BI "-endfit" " real" " -1"
+ Time where to end the exponential fit of the correlation function, -1 is till the end
+
--- /dev/null
+.TH genbox 1 "Tue 15 May 2001"
+.SH NAME
+genbox
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3genbox\fP
+.BI "-cp" " protein.gro "
+.BI "-cs" " spc216.gro "
+.BI "-ci" " insert.gro "
+.BI "-o" " out.gro "
+.BI "-p" " topol.top "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-box" " vector "
+.BI "-nmol" " int "
+.BI "-try" " int "
+.BI "-seed" " int "
+.BI "-vdwd" " real "
+.BI "-shell" " real "
+.SH DESCRIPTION
+Genbox can do one of 3 things:
+
+
+1) Generate a box of solvent. Specify -cs and -box. Or specify -cs and
+-cp with a structure file with a box, but without atoms.
+
+
+2) Solvate a solute configuration, eg. a protein, in a bath of solvent
+molecules. Specify
+.B -cp
+(solute) and
+.B -cs
+(solvent).
+The box specified in the solute coordinate file (
+.B -cp
+) is used,
+unless
+.B -box
+is set, which also centers the solute.
+The program
+.B editconf
+has more sophisticated options to change
+the box and center the solute.
+Solvent molecules are removed from the box where the
+distance between any atom of the solute molecule(s) and any atom of
+the solvent molecule is less than the sum of the VanderWaals radii of
+both atoms. A database (
+.B vdwradii.dat
+) of VanderWaals radii is
+read by the program, atoms not in the database are
+assigned a default distance
+.B -vdw
+.
+
+
+3) Insert a number (
+.B -nmol
+) of extra molecules (
+.B -ci
+)
+at random positions.
+The program iterates until
+.B nmol
+molecules
+have been inserted in the box. To test whether an insertion is
+successful the same VanderWaals criterium is used as for removal of
+solvent molecules. When no appropriately
+sized holes (holes that can hold an extra molecule) are available the
+program tries for
+.B -nmol
+*
+.B -try
+times before giving up.
+Increase -try if you have several small holes to fill.
+
+
+The default solvent is Simple Point Charge water (SPC). The coordinates
+for this are read from
+.B $GMXLIB/spc216.gro
+. Other
+solvents are also supported, as well as mixed solvents. The
+only restriction to solvent types is that a solvent molecule consists
+of exactly one residue. The residue information in the coordinate
+files is used, and should therefore be more or less consistent.
+In practice this means that two subsequent solvent molecules in the
+solvent coordinate file should have different residue number.
+The box of solute is built by stacking the coordinates read from
+the coordinate file. This means that these coordinates should be
+equlibrated in periodic boundary conditions to ensure a good
+alignment of molecules on the stacking interfaces.
+
+
+The program can optionally rotate the solute molecule to align the
+longest molecule axis along a box edge. This way the amount of solvent
+molecules necessary is reduced.
+It should be kept in mind that this only works for
+short simulations, as eg. an alpha-helical peptide in solution can
+rotate over 90 degrees, within 500 ps. In general it is therefore
+better to make a more or less cubic box.
+
+
+Setting -shell larger than zero will place a layer of water of
+the specified thickness (nm) around the solute. Hint: it is a good
+idea to put the protein in the center of a box first (using editconf).
+
+
+
+Finally, genbox will optionally remove lines from your topology file in
+which a number of solvent molecules is already added, and adds a
+line with the total number of solvent molecules in your coordinate file.
+.SH FILES
+.BI "-cp" " protein.gro"
+.B Input, Opt.
+ Generic structure: gro g96 pdb tpr tpb tpa
+
+.BI "-cs" " spc216.gro"
+.B Input, Opt., Lib.
+ Generic structure: gro g96 pdb tpr tpb tpa
+
+.BI "-ci" " insert.gro"
+.B Input, Opt.
+ Generic structure: gro g96 pdb tpr tpb tpa
+
+.BI "-o" " out.gro"
+.B Output
+ Generic structure: gro g96 pdb
+
+.BI "-p" " topol.top"
+.B In/Out, Opt.
+ Topology file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-box" " vector" " 0 0 0"
+ box size
+
+.BI "-nmol" " int" " 0"
+ no of extra molecules to insert
+
+.BI "-try" " int" " 10"
+ try inserting -nmol*-try times
+
+.BI "-seed" " int" " 1997"
+ random generator seed
+
+.BI "-vdwd" " real" " 0.105"
+ default vdwaals distance
+
+.BI "-shell" " real" " 0"
+ thickness of optional water layer around solute
+
+.SH DIAGNOSTICS
+\- Molecules must be whole in the initial configurations.
+
+\- At the moment -ci only works when inserting one molecule.
+
--- /dev/null
+.TH genconf 1 "Tue 15 May 2001"
+.SH NAME
+genconf
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3genconf\fP
+.BI "-f" " conf.gro "
+.BI "-o" " out.gro "
+.BI "-trj" " traj.xtc "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-nbox" " vector "
+.BI "-dist" " vector "
+.BI "-seed" " int "
+.BI "-[no]rot" ""
+.BI "-[no]shuffle" ""
+.BI "-[no]sort" ""
+.BI "-block" " int "
+.BI "-nmolat" " int "
+.BI "-maxrot" " vector "
+.BI "-[no]renumber" ""
+.SH DESCRIPTION
+genconf multiplies a given coordinate file by simply stacking them
+on top of each other, like a small child playing with wooden blocks.
+The program makes a grid of
+.I user defined
+
+proportions (
+.B -nbox
+),
+and interspaces the grid point with an extra space
+.B -dist
+.
+
+
+When option
+.B -rot
+is used the program does not check for overlap
+between molecules on grid points. It is recommended to make the box in
+the input file at least as big as the coordinates +
+Van der Waals radius.
+
+
+If the optional trajectory file is given, conformations are not
+generated, but read from this file and translated appropriately to
+build the grid.
+.SH FILES
+.BI "-f" " conf.gro"
+.B Input
+ Generic structure: gro g96 pdb tpr tpb tpa
+
+.BI "-o" " out.gro"
+.B Output
+ Generic structure: gro g96 pdb
+
+.BI "-trj" " traj.xtc"
+.B Input, Opt.
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 0"
+ Set the nicelevel
+
+.BI "-nbox" " vector" " 1 1 1"
+ Number of boxes
+
+.BI "-dist" " vector" " 0 0 0"
+ Distance between boxes
+
+.BI "-seed" " int" " 0"
+ Random generator seed, if 0 generated from the time
+
+.BI "-[no]rot" " no"
+ Randomly rotate conformations
+
+.BI "-[no]shuffle" " no"
+ Random shuffling of molecules
+
+.BI "-[no]sort" " no"
+ Sort molecules on X coord
+
+.BI "-block" " int" " 1"
+ Divide the box in blocks on this number of cpus
+
+.BI "-nmolat" " int" " 3"
+ Number of atoms per molecule, assumed to start from 0. If you set this wrong, it will screw up your system!
+
+.BI "-maxrot" " vector" " 90 90 90"
+ Maximum random rotation
+
+.BI "-[no]renumber" " no"
+ Renumber residues
+
+.SH DIAGNOSTICS
+\- The program should allow for random displacement off lattice points.
+
--- /dev/null
+.TH genion 1 "Tue 15 May 2001"
+.SH NAME
+genion
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3genion\fP
+.BI "-s" " topol.tpr "
+.BI "-n" " index.ndx "
+.BI "-o" " out.gro "
+.BI "-g" " genion.log "
+.BI "-pot" " pot.pdb "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-np" " int "
+.BI "-pname" " string "
+.BI "-pq" " real "
+.BI "-nn" " int "
+.BI "-nname" " string "
+.BI "-nq" " real "
+.BI "-rmin" " real "
+.BI "-[no]random" ""
+.BI "-seed" " int "
+.SH DESCRIPTION
+genion replaces solvent molecules by monoatomic ions at
+the position of the first atoms with the most favorable electrostatic
+potential or at random. The potential is calculated on all atoms, using
+normal GROMACS particle based methods (in contrast to other methods
+based on solving the Poisson-Boltzmann equation).
+The potential is recalculated after every ion insertion.
+If specified in the run input file, a reaction field or shift function
+can be used.
+The group of solvent molecules should be continuous and all molecules
+should have the same number of atoms.
+The user should add the ion molecules to the topology file and include
+the file
+.B ions.itp
+.
+Ion names for Gromos96 should include the charge.
+
+
+The potential can be written as B-factors
+in a pdb file (for visualisation using e.g. rasmol).
+The unit of the potential is 0.001 kJ/(mol e).
+
+
+For larger ions, e.g. sulfate we recommended to use genbox.
+.SH FILES
+.BI "-s" " topol.tpr"
+.B Input
+ Generic run input: tpr tpb tpa
+
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
+.BI "-o" " out.gro"
+.B Output
+ Generic structure: gro g96 pdb
+
+.BI "-g" " genion.log"
+.B Output
+ Log file
+
+.BI "-pot" " pot.pdb"
+.B Output, Opt.
+ Protein data bank file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-np" " int" " 0"
+ Number of positive ions
+
+.BI "-pname" " string" " Na"
+ Name of the positive ion
+
+.BI "-pq" " real" " 1"
+ Charge of the positive ion
+
+.BI "-nn" " int" " 0"
+ Number of negative ions
+
+.BI "-nname" " string" " Cl"
+ Name of the negative ion
+
+.BI "-nq" " real" " -1"
+ Charge of the negative ion
+
+.BI "-rmin" " real" " 0.6"
+ Minimum distance between ions
+
+.BI "-[no]random" " no"
+ Use random placement of ions instead of based on potential. The rmin option should still work
+
+.BI "-seed" " int" " 1993"
+ Seed for random number generator
+
--- /dev/null
+.TH genpr 1 "Tue 15 May 2001"
+.SH NAME
+genpr
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3genpr\fP
+.BI "-f" " conf.gro "
+.BI "-n" " index.ndx "
+.BI "-o" " posre.itp "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-fc" " vector "
+.SH DESCRIPTION
+genpr produces an include file for a topology containing
+a list of atom numbers and three force constants for the
+X, Y and Z direction. A single isotropic force constant may
+be given on the command line instead of three components.
+
+
+WARNING: genpr only works for the first molecule.
+Position restraints are interactions within molecules, therefore
+they should be included within the correct
+.B [ moleculetype ]
+
+block in the topology. Since the atom numbers in every moleculetype
+in the topology start at 1 and the numbers in the input file for
+genpr number consecutively from 1, genpr will only produce a useful
+file for the first molecule.
+.SH FILES
+.BI "-f" " conf.gro"
+.B Input
+ Generic structure: gro g96 pdb tpr tpb tpa
+
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
+.BI "-o" " posre.itp"
+.B Output
+ Include file for topology
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 0"
+ Set the nicelevel
+
+.BI "-fc" " vector" " 1000 1000 1000"
+ force constants (kJ mol-1 nm-2)
+
--- /dev/null
+.TH gmxcheck 1 "Tue 15 May 2001"
+.SH NAME
+gmxcheck
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3gmxcheck\fP
+.BI "-f" " traj.xtc "
+.BI "-f2" " traj.xtc "
+.BI "-s1" " top1.tpr "
+.BI "-s2" " top2.tpr "
+.BI "-c" " topol.tpr "
+.BI "-e" " ener.edr "
+.BI "-e2" " ener2.edr "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-vdwfac" " real "
+.BI "-bonlo" " real "
+.BI "-bonhi" " real "
+.BI "-tol" " real "
+.SH DESCRIPTION
+gmxcheck reads a trajectory (
+.B .trj
+,
+.B .trr
+or
+
+.B .xtc
+) or an energy file (
+.B .ene
+or
+.B .edr
+)
+and prints out useful information about them.
+
+
+Option
+.B -c
+checks for presence of coordinates,
+velocities and box in the file, for close contacts (smaller than
+
+.B -vdwfac
+and not bonded, i.e. not between
+.B -bonlo
+
+and
+.B -bonhi
+, all relative to the sum of both Van der Waals
+radii) and atoms outside the box (these may occur often and are
+no problem). If velocities are present, an estimated temperature
+will be calculated from them.
+
+
+The program will compare run input (
+.B .tpr
+,
+.B .tpb
+or
+
+.B .tpa
+) files
+when both
+.B -s1
+and
+.B -s2
+are supplied.
+.SH FILES
+.BI "-f" " traj.xtc"
+.B Input, Opt.
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-f2" " traj.xtc"
+.B Input, Opt.
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-s1" " top1.tpr"
+.B Input, Opt.
+ Generic run input: tpr tpb tpa
+
+.BI "-s2" " top2.tpr"
+.B Input, Opt.
+ Generic run input: tpr tpb tpa
+
+.BI "-c" " topol.tpr"
+.B Input, Opt.
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
+
+.BI "-e" " ener.edr"
+.B Input, Opt.
+ Generic energy: edr ene
+
+.BI "-e2" " ener2.edr"
+.B Input, Opt.
+ Generic energy: edr ene
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-vdwfac" " real" " 0.8"
+ Fraction of sum of VdW radii used as warning cutoff
+
+.BI "-bonlo" " real" " 0.4"
+ Min. fract. of sum of VdW radii for bonded atoms
+
+.BI "-bonhi" " real" " 0.7"
+ Max. fract. of sum of VdW radii for bonded atoms
+
+.BI "-tol" " real" " 0"
+ Tolerance for comparing real values
+
--- /dev/null
+.TH gmxdump 1 "Tue 15 May 2001"
+.SH NAME
+gmxdump
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3gmxdump\fP
+.BI "-s" " topol.tpr "
+.BI "-f" " traj.xtc "
+.BI "-e" " ener.edr "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-[no]nr" ""
+.SH DESCRIPTION
+gmxdump reads a run input file (
+.B .tpa
+/
+.B .tpr
+/
+.B .tpb
+),
+a trajectory (
+.B .trj
+/
+.B .trr
+/
+.B .xtc
+) or an energy
+file (
+.B .ene
+/
+.B .edr
+) and prints that to standard
+output in a readable format. This program is essential for
+checking your run input file in case of problems.
+
+
+.SH FILES
+.BI "-s" " topol.tpr"
+.B Input, Opt.
+ Generic run input: tpr tpb tpa
+
+.BI "-f" " traj.xtc"
+.B Input, Opt.
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-e" " ener.edr"
+.B Input, Opt.
+ Generic energy: edr ene
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 0"
+ Set the nicelevel
+
+.BI "-[no]nr" " yes"
+ Show index numbers in output (leaving them out makes comparison easier, but creates a useless topology)
+
--- /dev/null
+.TH grompp 1 "Tue 15 May 2001"
+.SH NAME
+grompp
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3grompp\fP
+.BI "-f" " grompp.mdp "
+.BI "-po" " mdout.mdp "
+.BI "-c" " conf.gro "
+.BI "-r" " conf.gro "
+.BI "-n" " index.ndx "
+.BI "-deshuf" " deshuf.ndx "
+.BI "-p" " topol.top "
+.BI "-pp" " processed.top "
+.BI "-o" " topol.tpr "
+.BI "-t" " traj.trr "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-[no]v" ""
+.BI "-time" " real "
+.BI "-np" " int "
+.BI "-[no]shuffle" ""
+.BI "-[no]sort" ""
+.BI "-[no]rmdumbds" ""
+.BI "-load" " string "
+.BI "-maxwarn" " int "
+.BI "-[no]check14" ""
+.SH DESCRIPTION
+The gromacs preprocessor
+reads a molecular topology file, checks the validity of the
+file, expands the topology from a molecular description to an atomic
+description. The topology file contains information about
+molecule types and the number of molecules, the preprocessor
+copies each molecule as needed.
+There is no limitation on the number of molecule types.
+Bonds and bond-angles can be converted into constraints, separately
+for hydrogens and heavy atoms.
+Then a coordinate file is read and velocities can be generated
+from a Maxwellian distribution if requested.
+grompp also reads parameters for the mdrun
+(eg. number of MD steps, time step, cut-off), and others such as
+NEMD parameters, which are corrected so that the net acceleration
+is zero.
+Eventually a binary file is produced that can serve as the sole input
+file for the MD program.
+
+
+grompp calls the c-preprocessor to resolve includes, macros
+etcetera. To specify a macro-preprocessor other than /lib/cpp
+(such as m4)
+you can put a line in your parameter file specifying the path
+to that cpp. Specifying
+.B -pp
+will get the pre-processed
+topology file written out.
+
+
+If your system does not have a c-preprocessor, you can still
+use grompp, but you do not have access to the features
+from the cpp. Command line options to the c-preprocessor can be given
+in the
+.B .mdp
+file. See your local manual (man cpp).
+
+
+When using position restraints a file with restraint coordinates
+can be supplied with
+.B -r
+, otherwise constraining will be done
+relative to the conformation from the
+.B -c
+option.
+
+
+Starting coordinates can be read from trajectory with
+.B -t
+.
+The last frame with coordinates and velocities will be read,
+unless the
+.B -time
+option is used.
+Note that these velocities will not be used when
+.B gen_vel = yes
+
+in your
+.B .mdp
+file. If you want to continue a crashed run, it is
+easier to use
+.B tpbconv
+.
+
+
+When preparing an input file for parallel
+.B mdrun
+it may
+be advantageous to partition the simulation system over the
+nodes in a way in which each node has a similar amount of
+work. The -shuffle option does just that. For a single protein
+in water this does not make a difference, however for a system where
+you have many copies of different molecules (e.g. liquid mixture
+or membrane/water system) the option is definitely a must.
+
+
+A further optimization for parallel systems is the
+.B -sort
+
+option which sorts molecules according to coordinates. This must
+always be used in conjunction with
+.B -shuffle
+, however
+sorting also works when you have only one molecule type.
+
+
+Using the
+.B -morse
+option grompp can convert the harmonic bonds
+in your topology to morse potentials. This makes it possible to break
+bonds. For this option to work you need an extra file in your $GMXLIB
+with dissociation energy. Use the -debug option to get more information
+on the workings of this option (look for MORSE in the grompp.log file
+using less or something like that).
+
+
+By default all bonded interactions which have constant energy due to
+dummy atom constructions will be removed. If this constant energy is
+not zero, this will result in a shift in the total energy. All bonded
+interactions can be kept by turning off
+.B -rmdumbds
+. Additionally,
+all constraints for distances which will be constant anyway because
+of dummy atom constructions will be removed. If any constraints remain
+which involve dummy atoms, a fatal error will result.
+
+To verify your run input file, please make notice of all warnings
+on the screen, and correct where necessary. Do also look at the contents
+of the
+.B mdout.mdp
+file, this contains comment lines, as well as
+the input that
+.B grompp
+has read. If in doubt you can start grompp
+with the
+.B -debug
+option which will give you more information
+in a file called grompp.log (along with real debug info). Finally, you
+can see the contents of the run input file with the
+.B gmxdump
+
+program.
+.SH FILES
+.BI "-f" " grompp.mdp"
+.B Input
+ grompp input file with MD parameters
+
+.BI "-po" " mdout.mdp"
+.B Output
+ grompp input file with MD parameters
+
+.BI "-c" " conf.gro"
+.B Input
+ Generic structure: gro g96 pdb tpr tpb tpa
+
+.BI "-r" " conf.gro"
+.B Input, Opt.
+ Generic structure: gro g96 pdb tpr tpb tpa
+
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
+.BI "-deshuf" " deshuf.ndx"
+.B Output, Opt.
+ Index file
+
+.BI "-p" " topol.top"
+.B Input
+ Topology file
+
+.BI "-pp" " processed.top"
+.B Output, Opt.
+ Topology file
+
+.BI "-o" " topol.tpr"
+.B Output
+ Generic run input: tpr tpb tpa
+
+.BI "-t" " traj.trr"
+.B Input, Opt.
+ Full precision trajectory: trr trj
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 0"
+ Set the nicelevel
+
+.BI "-[no]v" " yes"
+ Be loud and noisy
+
+.BI "-time" " real" " -1"
+ Take frame at or first after this time.
+
+.BI "-np" " int" " 1"
+ Generate statusfile for nodes
+
+.BI "-[no]shuffle" " no"
+ Shuffle molecules over nodes
+
+.BI "-[no]sort" " no"
+ Sort molecules according to X coordinate
+
+.BI "-[no]rmdumbds" " yes"
+ Remove constant bonded interactions with dummies
+
+.BI "-load" " string" " "
+ Releative load capacity of each node on a parallel machine. Be sure to use quotes around the string, which should contain a number for each node
+
+.BI "-maxwarn" " int" " 10"
+ Number of warnings after which input processing stops
+
+.BI "-[no]check14" " no"
+ Remove 1-4 interactions without Van der Waals
+
--- /dev/null
+.TH highway 1 "Tue 15 May 2001"
+.SH NAME
+highway
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3highway\fP
+.BI "-f" " highway.dat "
+.BI "-a" " auto.dat "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.SH DESCRIPTION
+highway is the gromacs highway simulator. It is an X-windows
+gadget that shows a (periodic) autobahn with a user defined
+number of cars. Fog can be turned on or off to increase the
+number of crashes. Nice for a background CPU-eater
+.SH FILES
+.BI "-f" " highway.dat"
+.B Input
+ Generic data file
+
+.BI "-a" " auto.dat"
+.B Input
+ Generic data file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 0"
+ Set the nicelevel
+
+.BI "-b" " time" " -1"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " -1"
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " -1"
+ Only use frame when t MOD dt = first time (ps)
+
--- /dev/null
+.TH make_ndx 1 "Tue 15 May 2001"
+.SH NAME
+make_ndx
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3make_ndx\fP
+.BI "-f" " conf.gro "
+.BI "-n" " index.ndx "
+.BI "-o" " index.ndx "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.SH DESCRIPTION
+Index groups are necessary for almost every gromacs program.
+All these programs can generate default index groups. You ONLY
+have to use make_ndx when you need SPECIAL index groups.
+There is a default index group for the whole system, 9 default
+index groups are generated for proteins, a default index group
+is generated for every other residue name.
+
+When no index file is supplied, also make_ndx will generate the
+default groups.
+With the index editor you can select on atom, residue and chain names
+and numbers, you can use NOT, AND and OR, you can split groups
+into chains, residues or atoms. You can delete and rename groups.
+
+
+The atom numbering in the editor and the index file starts at 1.
+.SH FILES
+.BI "-f" " conf.gro"
+.B Input
+ Generic structure: gro g96 pdb tpr tpb tpa
+
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
+.BI "-o" " index.ndx"
+.B Output
+ Index file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 0"
+ Set the nicelevel
+
--- /dev/null
+.TH mdrun 1 "Tue 15 May 2001"
+.SH NAME
+mdrun
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3mdrun\fP
+.BI "-s" " topol.tpr "
+.BI "-o" " traj.trr "
+.BI "-x" " traj.xtc "
+.BI "-c" " confout.gro "
+.BI "-e" " ener.edr "
+.BI "-g" " md.log "
+.BI "-dgdl" " dgdl.xvg "
+.BI "-table" " table.xvg "
+.BI "-rerun" " rerun.xtc "
+.BI "-ei" " sam.edi "
+.BI "-eo" " sam.edo "
+.BI "-pi" " pull.ppa "
+.BI "-po" " pullout.ppa "
+.BI "-pd" " pull.pdo "
+.BI "-pn" " pull.ndx "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-deffnm" " string "
+.BI "-[no]v" ""
+.BI "-[no]compact" ""
+.SH DESCRIPTION
+The mdrun program performs Molecular Dynamics simulations.
+It reads the run input file (
+.B -s
+) and distributes the
+topology over nodes if needed. The coordinates are passed
+around, so that computations can begin.
+First a neighborlist is made, then the forces are computed.
+The forces are globally summed, and the velocities and
+positions are updated. If necessary shake is performed to constrain
+bond lengths and/or bond angles.
+Temperature and Pressure can be controlled using weak coupling to a
+bath.
+
+
+mdrun produces at least three output file, plus one log file
+(
+.B -g
+) per node.
+The trajectory file (
+.B -o
+), contains coordinates, velocities and
+optionally forces.
+The structure file (
+.B -c
+) contains the coordinates and
+velocities of the last step.
+The energy file (
+.B -e
+) contains energies, the temperature,
+pressure, etc, a lot of these things are also printed in the log file
+of node 0.
+Optionally coordinates can be written to a compressed trajectory file
+(
+.B -x
+).
+
+
+When running in parallel with PVM or an old version of MPI the
+
+.B -np
+option must be given to indicate the number of
+nodes.
+
+
+The option
+.B -dgdl
+is only used when free energy perturbation is
+turned on.
+
+
+With
+.B -rerun
+an input trajectory can be given for which
+forces and energies will be (re)calculated. Neighbor searching will be
+performed for every frame, unless
+.B nstlist
+is zero
+(see the
+.B .mdp
+file).
+
+
+ED (essential dynamics) sampling is switched on by using the
+.B -ei
+
+flag followed by an
+.B .edi
+file.
+The
+.B .edi
+file can be produced using options in the essdyn
+menu of the WHAT IF program. mdrun produces a
+.B .edo
+file that
+contains projections of positions, velocities and forces onto selected
+eigenvectors.
+
+
+The -table option can be used to pass mdrun a formatted table with
+user-defined potential functions. The file is read from either the
+current directory or from the GMXLIB directory. A number of preformatted
+tables are presented in the GMXLIB dir, for 6-8, 6-9, 6-10, 6-11, 6-12
+Lennard Jones potentials with normal Coulomb.
+
+
+The options
+.B -pi
+,
+.B -po
+,
+.B -pd
+,
+.B -pn
+are used
+for potential of mean force calculations and umbrella sampling.
+See manual.
+
+
+When mdrun receives a TERM signal, it will set nsteps to the current
+step plus one. When mdrun receives a USR1 signal, it will set nsteps
+to the next multiple of nstxout after the current step.
+In both cases all the usual output will be written to file.
+When running with MPI, a signal to one of the mdrun processes
+is sufficient, this signal should not be sent to mpirun or
+the mdrun process that is the parent of the others.
+.SH FILES
+.BI "-s" " topol.tpr"
+.B Input
+ Generic run input: tpr tpb tpa
+
+.BI "-o" " traj.trr"
+.B Output
+ Full precision trajectory: trr trj
+
+.BI "-x" " traj.xtc"
+.B Output, Opt.
+ Compressed trajectory (portable xdr format)
+
+.BI "-c" " confout.gro"
+.B Output
+ Generic structure: gro g96 pdb
+
+.BI "-e" " ener.edr"
+.B Output
+ Generic energy: edr ene
+
+.BI "-g" " md.log"
+.B Output
+ Log file
+
+.BI "-dgdl" " dgdl.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-table" " table.xvg"
+.B Input, Opt.
+ xvgr/xmgr file
+
+.BI "-rerun" " rerun.xtc"
+.B Input, Opt.
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-ei" " sam.edi"
+.B Input, Opt.
+ ED sampling input
+
+.BI "-eo" " sam.edo"
+.B Output, Opt.
+ ED sampling output
+
+.BI "-pi" " pull.ppa"
+.B Input, Opt.
+ Pull parameters
+
+.BI "-po" " pullout.ppa"
+.B Output, Opt.
+ Pull parameters
+
+.BI "-pd" " pull.pdo"
+.B Output, Opt.
+ Pull data output
+
+.BI "-pn" " pull.ndx"
+.B Input, Opt.
+ Index file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-deffnm" " string" " "
+ Set the default filename for all file options
+
+.BI "-[no]v" " no"
+ Be loud and noisy
+
+.BI "-[no]compact" " yes"
+ Write a compact log file
+
--- /dev/null
+.TH mk_angndx 1 "Tue 15 May 2001"
+.SH NAME
+mk_angndx
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3mk_angndx\fP
+.BI "-s" " topol.tpr "
+.BI "-n" " angle.ndx "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-type" " enum "
+.SH DESCRIPTION
+mk_angndx makes an index file for calculation of
+angle distributions etc. It uses a run input file (
+.B .tpx
+) for the
+definitions of the angles, dihedrals etc.
+.SH FILES
+.BI "-s" " topol.tpr"
+.B Input
+ Generic run input: tpr tpb tpa
+
+.BI "-n" " angle.ndx"
+.B Output
+ Index file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 0"
+ Set the nicelevel
+
+.BI "-type" " enum" " angle"
+ Type of angle: angle, g96-angle, dihedral, improper, ryckaert-bellemans or phi-psi
+
--- /dev/null
+.TH ngmx 1 "Tue 15 May 2001"
+.SH NAME
+ngmx
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3ngmx\fP
+.BI "-f" " traj.xtc "
+.BI "-s" " topol.tpr "
+.BI "-n" " index.ndx "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.SH DESCRIPTION
+ngmx is the Gromacs trajectory viewer. This program reads a
+trajectory file, a run input file and an index file and plots a
+3D structure of your molecule on your standard X Window
+screen. No need for a high end graphics workstation, it even
+works on Monochrome screens.
+
+
+The following features have been implemented:
+3D view, rotation, translation and scaling of your molecule(s),
+labels on atoms, animation of trajectories,
+hardcopy in PostScript format, user defined atom-filters
+runs on MIT-X (real X), open windows and motif,
+user friendly menus, option to remove periodicity, option to
+show computational box.
+
+
+Some of the more common X command line options can be used:
+
+-bg, -fg change colors, -font fontname, changes the font.
+.SH FILES
+.BI "-f" " traj.xtc"
+.B Input
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-s" " topol.tpr"
+.B Input
+ Generic run input: tpr tpb tpa
+
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 0"
+ Set the nicelevel
+
+.BI "-b" " time" " -1"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " -1"
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " -1"
+ Only use frame when t MOD dt = first time (ps)
+
+.SH DIAGNOSTICS
+\- Balls option does not work
+
+\- Some times dumps core without a good reason
+
--- /dev/null
+.TH nmrun 1 "Tue 15 May 2001"
+.SH NAME
+nmrun
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3nmrun\fP
+.BI "-s" " topol.tpr "
+.BI "-m" " hessian.mtx "
+.BI "-g" " nm.log "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-[no]v" ""
+.BI "-[no]compact" ""
+.SH DESCRIPTION
+nmrun builds a Hessian matrix from single conformation.
+For usual Normal Modes-like calculations, make sure that
+the structure provided is properly energy-minimised.
+The generated matrix can be diagonalized by g_nmeig.
+.SH FILES
+.BI "-s" " topol.tpr"
+.B Input
+ Generic run input: tpr tpb tpa
+
+.BI "-m" " hessian.mtx"
+.B Output
+ Hessian matrix
+
+.BI "-g" " nm.log"
+.B Output
+ Log file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-[no]v" " no"
+ Verbose mode
+
+.BI "-[no]compact" " yes"
+ Write a compact log file
+
--- /dev/null
+.TH pdb2gmx 1 "Tue 15 May 2001"
+.SH NAME
+pdb2gmx
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3pdb2gmx\fP
+.BI "-f" " eiwit.pdb "
+.BI "-o" " conf.gro "
+.BI "-p" " topol.top "
+.BI "-i" " posre.itp "
+.BI "-n" " clean.ndx "
+.BI "-q" " clean.pdb "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-[no]merge" ""
+.BI "-[no]inter" ""
+.BI "-[no]ss" ""
+.BI "-[no]ter" ""
+.BI "-[no]lys" ""
+.BI "-[no]asp" ""
+.BI "-[no]glu" ""
+.BI "-[no]his" ""
+.BI "-angle" " real "
+.BI "-dist" " real "
+.BI "-[no]una" ""
+.BI "-[no]sort" ""
+.BI "-[no]H14" ""
+.BI "-[no]ignh" ""
+.BI "-[no]alldih" ""
+.BI "-dummy" " enum "
+.BI "-[no]heavyh" ""
+.BI "-[no]deuterate" ""
+.SH DESCRIPTION
+This program reads a pdb file, lets you choose a forcefield, reads
+some database files, adds hydrogens to the molecules and generates
+coordinates in Gromacs (Gromos) format and a topology in Gromacs format.
+These files can subsequently be processed to generate a run input file.
+
+
+
+Note that a pdb file is nothing more than a file format, and it
+need not necessarily contain a protein structure. Every kind of
+molecule for which there is support in the database can be converted.
+If there is no support in the database, you can add it yourself.
+
+
+The program has limited intelligence, it reads a number of database
+files, that allow it to make special bonds (Cys-Cys, Heme-His, etc.),
+if necessary this can be done manually. The program can prompt the
+user to select which kind of LYS, ASP, GLU, CYS or HIS residue she
+wants. For LYS the choice is between LYS (two protons on NZ) or LYSH
+(three protons, default), for ASP and GLU unprotonated (default) or
+protonated, for HIS the proton can be either on ND1 (HISA), on NE2
+(HISB) or on both (HISH). By default these selections are done
+automatically. For His, this is based on an optimal hydrogen bonding
+conformation. Hydrogen bonds are defined based on a simple geometric
+criterium, specified by the maximum hydrogen-donor-acceptor angle
+and donor-acceptor distance, which are set by
+.B -angle
+and
+
+.B -dist
+respectively.
+
+
+Option
+.B -merge
+will ask if you want to merge consecutive chains
+into one molecule, this can be useful for connecting chains with a
+disulfide brigde.
+
+
+pdb2gmx will also check the occupancy field of the pdb file.
+If any of the occupanccies are not one, indicating that the atom is
+not resolved well in the structure, a warning message is issued.
+When a pdb file does not originate from an X-Ray structure determination
+all occupancy fields may be zero. Either way, it is up to the user
+to verify the correctness of the input data (read the article!).
+
+
+During processing the atoms will be reordered according to Gromacs
+conventions. With
+.B -n
+an index file can be generated that
+contains one group reordered in the same way. This allows you to
+convert a Gromos trajectory and coordinate file to Gromos. There is
+one limitation: reordering is done after the hydrogens are stripped
+from the input and before new hydrogens are added. This means that
+you should not use
+.B -ignh
+.
+
+
+The
+.B .gro
+and
+.B .g96
+file formats do not support chain
+identifiers. Therefore it is useful to enter a pdb file name at
+the
+.B -o
+option when you want to convert a multichain pdb file.
+
+
+
+
+.B -sort
+will sort all residues according to the order in the
+database, sometimes this is necessary to get charge groups
+together.
+
+
+
+.B -alldih
+will generate all proper dihedrals instead of only
+those with as few hydrogens as possible, this is useful for use with
+the Charmm forcefield.
+
+
+The option
+.B -dummy
+removes hydrogen and fast improper dihedral
+motions. Angular and out-of-plane motions can be removed by changing
+hydrogens into dummy atoms and fixing angles, which fixes their
+position relative to neighboring atoms. Additionally, all atoms in the
+aromatic rings of the standard amino acids (i.e. PHE, TRP, TYR and HIS)
+can be converted into dummy atoms, elminating the fast improper dihedral
+fluctuations in these rings. Note that in this case all other hydrogen
+atoms are also converted to dummy atoms. The mass of all atoms that are
+converted into dummy atoms, is added to the heavy atoms.
+
+
+Also slowing down of dihedral motion can be done with
+.B -heavyh
+
+done by increasing the hydrogen-mass by a factor of 4. This is also
+done for water hydrogens to slow down the rotational motion of water.
+The increase in mass of the hydrogens is subtracted from the bonded
+(heavy) atom so that the total mass of the system remains the same.
+Reference Feenstra et al., J. Comput. Chem. 20, 786 (1999).
+.SH FILES
+.BI "-f" " eiwit.pdb"
+.B Input
+ Generic structure: gro g96 pdb tpr tpb tpa
+
+.BI "-o" " conf.gro"
+.B Output
+ Generic structure: gro g96 pdb
+
+.BI "-p" " topol.top"
+.B Output
+ Topology file
+
+.BI "-i" " posre.itp"
+.B Output
+ Include file for topology
+
+.BI "-n" " clean.ndx"
+.B Output, Opt.
+ Index file
+
+.BI "-q" " clean.pdb"
+.B Output, Opt.
+ Generic structure: gro g96 pdb
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 0"
+ Set the nicelevel
+
+.BI "-[no]merge" " no"
+ Merge multiple chains into one molecule
+
+.BI "-[no]inter" " no"
+ Set the next 6 options to interactive
+
+.BI "-[no]ss" " no"
+ Interactive SS bridge selection
+
+.BI "-[no]ter" " no"
+ Interactive termini selection, iso charged
+
+.BI "-[no]lys" " no"
+ Interactive Lysine selection, iso charged
+
+.BI "-[no]asp" " no"
+ Interactive Aspartic Acid selection, iso charged
+
+.BI "-[no]glu" " no"
+ Interactive Glutamic Acid selection, iso charged
+
+.BI "-[no]his" " no"
+ Interactive Histidine selection, iso checking H-bonds
+
+.BI "-angle" " real" " 135"
+ Minimum hydrogen-donor-acceptor angle for a H-bond (degrees)
+
+.BI "-dist" " real" " 0.3"
+ Maximum donor-acceptor distance for a H-bond (nm)
+
+.BI "-[no]una" " no"
+ Select aromatic rings with united CH atoms on Phenylalanine, Tryptophane and Tyrosine
+
+.BI "-[no]sort" " yes"
+ Sort the residues according to database
+
+.BI "-[no]H14" " no"
+ Use 1-4 interactions between hydrogen atoms
+
+.BI "-[no]ignh" " no"
+ Ignore hydrogen atoms that are in the pdb file
+
+.BI "-[no]alldih" " no"
+ Generate all proper dihedrals
+
+.BI "-dummy" " enum" " none"
+ Convert atoms to dummy atoms: none, hydrogens or aromatics
+
+.BI "-[no]heavyh" " no"
+ Make hydrogen atoms heavy
+
+.BI "-[no]deuterate" " no"
+ Change the mass of hydrogens to 2 amu
+
--- /dev/null
+.TH protonate 1 "Tue 15 May 2001"
+.SH NAME
+protonate
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3protonate\fP
+.BI "-s" " topol.tpr "
+.BI "-f" " traj.xtc "
+.BI "-n" " index.ndx "
+.BI "-o" " protonated.xtc "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.SH DESCRIPTION
+
+.B protonate
+reads (a) conformation(s) and adds all missing
+hydrogens as defined in
+.B ffgmx2.hdb
+. If only
+.B -s
+is
+specified, this conformation will be protonated, if also
+.B -f
+
+is specified, the conformation(s) will be read from this file
+which can be either a single conformation or a trajectory.
+
+
+
+If a pdb file is supplied, residue names might not correspond to
+to the GROMACS naming conventions, in which case these residues will
+probably not be properly protonated.
+
+
+
+If an index file is specified, please note that the atom numbers
+should correspond to the
+.B protonated
+state.
+.SH FILES
+.BI "-s" " topol.tpr"
+.B Input
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
+
+.BI "-f" " traj.xtc"
+.B Input, Opt.
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
+.BI "-o" " protonated.xtc"
+.B Output
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 0"
+ Set the nicelevel
+
+.BI "-b" " time" " -1"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " -1"
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " -1"
+ Only use frame when t MOD dt = first time (ps)
+
--- /dev/null
+.TH tpbconv 1 "Tue 15 May 2001"
+.SH NAME
+tpbconv
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3tpbconv\fP
+.BI "-s" " topol.tpr "
+.BI "-f" " traj.trr "
+.BI "-n" " index.ndx "
+.BI "-o" " tpxout.tpr "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-time" " real "
+.BI "-extend" " real "
+.BI "-until" " real "
+.BI "-[no]unconstrained" ""
+.SH DESCRIPTION
+tpbconv can edit run input files in two ways.
+
+
+.B 1st.
+by creating a run input file
+for a continuation run when your simulation has crashed due to e.g.
+a full disk, or by making a continuation run input file.
+Note that a frame with coordinates and velocities is needed,
+which means that when you never write velocities, you can not use
+tpbconv and you have to start the run again from the beginning.
+
+
+
+.B 2nd.
+by creating a tpx file for a subset of your original
+tpx file, which is useful when you want to remove the solvent from
+your tpx file, or when you want to make e.g. a pure Ca tpx file.
+
+.B WARNING: this tpx file is not fully functional
+.
+.SH FILES
+.BI "-s" " topol.tpr"
+.B Input
+ Generic run input: tpr tpb tpa
+
+.BI "-f" " traj.trr"
+.B Input, Opt.
+ Full precision trajectory: trr trj
+
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
+.BI "-o" " tpxout.tpr"
+.B Output
+ Generic run input: tpr tpb tpa
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 0"
+ Set the nicelevel
+
+.BI "-time" " real" " -1"
+ Continue from frame at this time (ps) instead of the last frame
+
+.BI "-extend" " real" " 0"
+ Extend runtime by this amount (ps)
+
+.BI "-until" " real" " 0"
+ Extend runtime until this ending time (ps)
+
+.BI "-[no]unconstrained" " yes"
+ For a continuous trajectory, the constraints should not be solved before the first step (default)
+
--- /dev/null
+.TH trjcat 1 "Tue 15 May 2001"
+.SH NAME
+trjcat
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3trjcat\fP
+.BI "-o" " trajout.xtc "
+.BI "-n" " index.ndx "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-b" " real "
+.BI "-e" " real "
+.BI "-dt" " real "
+.BI "-prec" " int "
+.BI "-[no]vel" ""
+.BI "-[no]settime" ""
+.BI "-[no]sort" ""
+.SH DESCRIPTION
+trjcat concatenates several input trajectory files in sorted order.
+In case of double time frames the one in the later file is used.
+By specifying
+.B -settime
+you will be asked for the start time
+of each file. The input files are taken from the command line,
+such that a command like
+.B trjcat -o fixed.trr *.trr
+should do
+the trick.
+.SH FILES
+.BI "-o" " trajout.xtc"
+.B Output
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " real" " -1"
+ First time to use
+
+.BI "-e" " real" " -1"
+ Last time to use
+
+.BI "-dt" " real" " 0"
+ Only write frame when t MOD dt = first time
+
+.BI "-prec" " int" " 3"
+ Precision for .xtc and .gro writing in number of decimal places
+
+.BI "-[no]vel" " yes"
+ Read and write velocities if possible
+
+.BI "-[no]settime" " no"
+ Change starting time interactively
+
+.BI "-[no]sort" " yes"
+ Sort trajectory files (not frames)
+
--- /dev/null
+.TH trjconv 1 "Tue 15 May 2001"
+.SH NAME
+trjconv
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3trjconv\fP
+.BI "-f" " traj.xtc "
+.BI "-o" " trajout.xtc "
+.BI "-s" " topol.tpr "
+.BI "-n" " index.ndx "
+.BI "-fr" " frames.ndx "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-tu" " enum "
+.BI "-[no]w" ""
+.BI "-skip" " int "
+.BI "-dt" " time "
+.BI "-dump" " time "
+.BI "-t0" " time "
+.BI "-timestep" " time "
+.BI "-pbc" " enum "
+.BI "-ur" " enum "
+.BI "-[no]center" ""
+.BI "-box" " vector "
+.BI "-shift" " vector "
+.BI "-[no]fit" ""
+.BI "-[no]pfit" ""
+.BI "-ndec" " int "
+.BI "-[no]vel" ""
+.BI "-[no]force" ""
+.BI "-trunc" " time "
+.BI "-exec" " string "
+.BI "-[no]app" ""
+.BI "-[no]sep" ""
+.SH DESCRIPTION
+trjconv can convert trajectory files in many ways:
+
+
+.B 1.
+from one format to another
+
+
+.B 2.
+select a subset of atoms
+
+
+.B 3.
+remove periodicity from molecules
+
+
+.B 4.
+keep multimeric molecules together
+
+
+.B 5.
+center atoms in the box
+
+
+.B 6.
+fit atoms to reference structure
+
+
+.B 7.
+reduce the number of frames
+
+
+.B 8.
+change the timestamps of the frames
+(
+.B -t0
+and
+.B -timestep
+)
+
+
+
+The program
+.B trjcat
+can concatenate multiple trajectory files.
+
+
+
+Currently seven formats are supported for input and output:
+
+.B .xtc
+,
+.B .trr
+,
+.B .trj
+,
+.B .gro
+,
+.B .g96
+,
+
+.B .pdb
+and
+.B .g87
+.
+The file formats are detected from the file extension.
+The precision of
+.B .xtc
+and
+.B .gro
+output is taken from the
+input file for
+.B .xtc
+,
+.B .gro
+and
+.B .pdb
+,
+and from the
+.B -ndec
+option for other input formats. The precision
+is always taken from
+.B -ndec
+, when this option is set.
+All other formats have fixed precision.
+.B .trr
+and
+.B .trj
+
+output can be single or double precision, depending on the precision
+of the trjconv binary.
+Note that velocities are only supported in
+
+.B .trr
+,
+.B .trj
+,
+.B .gro
+and
+.B .g96
+files.
+
+
+Option
+.B -app
+can be used to
+append output to an existing trajectory file.
+No checks are performed to ensure integrity
+of the resulting combined trajectory file.
+
+.B .pdb
+files with all frames concatenated can be viewed with
+
+.B rasmol -nmrpdb
+.
+
+
+It is possible to select part of your trajectory and write it out
+to a new trajectory file in order to save disk space, e.g. for leaving
+out the water from a trajectory of a protein in water.
+
+.B ALWAYS
+put the original trajectory on tape!
+We recommend to use the portable
+.B .xtc
+format for your analysis
+to save disk space and to have portable files.
+
+
+There are two options for fitting the trajectory to a reference
+either for essential dynamics analysis or for whatever.
+The first option is just plain fitting to a reference structure
+in the structure file, the second option is a progressive fit
+in which the first timeframe is fitted to the reference structure
+in the structure file to obtain and each subsequent timeframe is
+fitted to the previously fitted structure. This way a continuous
+trajectory is generated, which might not be the case when using the
+regular fit method, e.g. when your protein undergoes large
+conformational transitions.
+
+
+Option
+.B -pbc
+sets the type of periodic boundary condition
+treatment.
+.B whole
+puts the atoms in the box and then makes
+broken molecules whole (a run input file is required).
+
+.B inbox
+puts all the atoms in the box.
+
+.B nojump
+checks if atoms jump across the box and then puts
+them back. This has the effect that all molecules
+will remain whole (provided they were whole in the initial
+conformation), note that this ensures a continuous trajectory but
+molecules may diffuse out of the box. The starting configuration
+for this procedure is taken from the structure file, if one is
+supplied, otherwise it is the first frame.
+
+.B -pbc
+is ignored when
+.B -fit
+of
+.B -pfit
+is set,
+in that case molecules will be made whole.
+
+
+Option
+.B -ur
+sets the unit cell representation for options
+
+.B whole
+and
+.B inbox
+of
+.B -pbc
+.
+All three options give different results for triclinc boxes and
+identical results for rectangular boxes.
+
+.B rect
+is the ordinary brick shape.
+
+.B tric
+is the triclinic unit cell.
+
+.B compact
+puts all atoms at the closest distance from the center
+of the box. This can be useful for visualizing e.g. truncated
+octahedrons.
+
+
+Option
+.B -center
+centers the system in the box. The user can
+select the group which is used to determine the geometrical center.
+Use option
+.B -pbc whole
+in addition to
+.B -center
+when you
+want all molecules in the box after the centering.
+
+
+With
+.B -dt
+it is possible to reduce the number of
+frames in the output. This option relies on the accuracy of the times
+in your input trajectory, so if these are inaccurate use the
+
+.B -timestep
+
+option to modify the time (this can be done simultaneously).
+
+
+Using
+.B -trunc
+trjconv can truncate
+.B .trj
+in place, i.e.
+without copying the file. This is useful when a run has crashed
+during disk I/O (one more disk full), or when two contiguous
+trajectories must be concatenated without have double frames.
+
+
+
+.B trjcat
+is more suitable for concatenating trajectory files.
+
+
+Option
+.B -dump
+can be used to extract a frame at or near
+one specific time from your trajectory.
+.SH FILES
+.BI "-f" " traj.xtc"
+.B Input
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-o" " trajout.xtc"
+.B Output
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-s" " topol.tpr"
+.B Input, Opt.
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
+
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
+.BI "-fr" " frames.ndx"
+.B Input, Opt.
+ Index file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " -1"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " -1"
+ Last frame (ps) to read from trajectory
+
+.BI "-tu" " enum" " ps"
+ Time unit: ps, fs, ns, us, ms, s, m or h
+
+.BI "-[no]w" " no"
+ View output xvg, xpm, eps and pdb files
+
+.BI "-skip" " int" " 1"
+ Only write every nr-th frame
+
+.BI "-dt" " time" " 0"
+ Only write frame when t MOD dt = first time (ps)
+
+.BI "-dump" " time" " -1"
+ Dump frame nearest specified time (ps)
+
+.BI "-t0" " time" " 0"
+ Starting time (ps) (default: don't change)
+
+.BI "-timestep" " time" " 0"
+ Change time step between input frames (ps)
+
+.BI "-pbc" " enum" " none"
+ PBC treatment: none, whole, inbox or nojump
+
+.BI "-ur" " enum" " rect"
+ Unit-cell representation: rect, tric or compact
+
+.BI "-[no]center" " no"
+ Center atoms in box
+
+.BI "-box" " vector" " 0 0 0"
+ Size for new cubic box (default: read from input)
+
+.BI "-shift" " vector" " 0 0 0"
+ All coordinates will be shifted by framenr*shift
+
+.BI "-[no]fit" " no"
+ Fit molecule to ref structure in the structure file
+
+.BI "-[no]pfit" " no"
+ Progressive fit, to the previous fitted structure
+
+.BI "-ndec" " int" " 3"
+ Precision for .xtc and .gro writing in number of decimal places
+
+.BI "-[no]vel" " yes"
+ Read and write velocities if possible
+
+.BI "-[no]force" " no"
+ Read and write forces if possible
+
+.BI "-trunc" " time" " -1"
+ Truncate input trj file after this time (ps)
+
+.BI "-exec" " string" " "
+ Execute command for every output frame with the frame number as argument
+
+.BI "-[no]app" " no"
+ Append output
+
+.BI "-[no]sep" " no"
+ Write each frame to a separate .gro or .pdb file
+
--- /dev/null
+.TH trjorder 1 "Tue 15 May 2001"
+.SH NAME
+trjorder
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3trjorder\fP
+.BI "-f" " traj.xtc "
+.BI "-s" " topol.tpr "
+.BI "-n" " index.ndx "
+.BI "-o" " ordered.xtc "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-na" " int "
+.BI "-da" " int "
+.SH DESCRIPTION
+trjorder orders molecules according to the smallest distance
+to atoms in a reference group. It will ask for a group of reference
+atoms and a group of molecules. For each frame of the trajectory
+the selected molecules will be reordered according to the shortest
+distance between atom number
+.B -da
+in the molecule and all the
+atoms in the reference group. All atoms in the trajectory are written
+to the output trajectory.
+
+
+trjorder can be useful for e.g. analyzing the n waters closest to a
+protein.
+In that case the reference group would be the protein and the group
+of molecules would consist of all the water atoms. When an index group
+of the first n waters is made, the ordered trajectory can be used
+with any Gromacs program to analyze the n closest waters.
+.SH FILES
+.BI "-f" " traj.xtc"
+.B Input
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-s" " topol.tpr"
+.B Input
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
+
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
+.BI "-o" " ordered.xtc"
+.B Output
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " -1"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " -1"
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " -1"
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-na" " int" " 3"
+ Number of atoms in a molecule
+
+.BI "-da" " int" " 1"
+ Atom used for the distance calculation
+
--- /dev/null
+.TH wheel 1 "Tue 15 May 2001"
+.SH NAME
+wheel
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3wheel\fP
+.BI "-f" " nnnice.dat "
+.BI "-o" " plot.eps "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-r0" " int "
+.BI "-rot0" " real "
+.BI "-T" " string "
+.BI "-[no]nn" ""
+.SH DESCRIPTION
+wheel plots a helical wheel representation of your sequence.The input sequence is in the .dat file where the first line contains
+the number of residues and each consecutive line contains a residuename.
+.SH FILES
+.BI "-f" " nnnice.dat"
+.B Input
+ Generic data file
+
+.BI "-o" " plot.eps"
+.B Output
+ Encapsulated PostScript (tm) file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-r0" " int" " 1"
+ The first residue number in the sequence
+
+.BI "-rot0" " real" " 0"
+ Rotate around an angle initially (90 degrees makes sense)
+
+.BI "-T" " string" " "
+ Plot a title in the center of the wheel (must be shorter than 10 characters, or it will overwrite the wheel)
+
+.BI "-[no]nn" " yes"
+ Toggle numbers
+
--- /dev/null
+.TH x2top 1 "Tue 15 May 2001"
+.SH NAME
+x2top
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3x2top\fP
+.BI "-f" " conf.gro "
+.BI "-o" " out.top "
+.BI "-r" " out.rtp "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-kb" " real "
+.BI "-kt" " real "
+.BI "-kp" " real "
+.BI "-nexcl" " int "
+.BI "-[no]H14" ""
+.BI "-[no]alldih" ""
+.BI "-[no]round" ""
+.BI "-[no]pairs" ""
+.BI "-name" " string "
+.SH DESCRIPTION
+x2top generates a primitive topology from a coordinate file.
+The program assumes all hydrogens are present when defining
+the hybridization from the atom name and the number of bonds.
+The program can also make an rtp entry, which you can then add
+to the rtp database.
+.SH FILES
+.BI "-f" " conf.gro"
+.B Input
+ Generic structure: gro g96 pdb tpr tpb tpa
+
+.BI "-o" " out.top"
+.B Output, Opt.
+ Topology file
+
+.BI "-r" " out.rtp"
+.B Output, Opt.
+ Residue Type file used by pdb2gmx
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 0"
+ Set the nicelevel
+
+.BI "-kb" " real" " 400000"
+ Bonded force constant (kJ/mol/nm2)
+
+.BI "-kt" " real" " 400"
+ Angle force constant (kJ/mol/rad2)
+
+.BI "-kp" " real" " 5"
+ Dihedral angle force constant (kJ/mol/rad2)
+
+.BI "-nexcl" " int" " 3"
+ Number of exclusions
+
+.BI "-[no]H14" " no"
+ Use 3rd neighbour interactions for hydrogen atoms
+
+.BI "-[no]alldih" " no"
+ Generate all proper dihedrals
+
+.BI "-[no]round" " yes"
+ Round off measured values
+
+.BI "-[no]pairs" " yes"
+ Output 1-4 interactions (pairs) in topology file
+
+.BI "-name" " string" " ICE"
+ Name of your molecule
+
+.SH DIAGNOSTICS
+\- The atom type selection is primitive. Virtually no chemical knowledge is used
+
+\- Periodic boundary conditions screw up the bonding
+
+\- No improper dihedrals are generated
+
+\- The atoms to atomtype translation table is incomplete (ffG43a1.n2t file in the $GMXLIB directory). Please extend it and send the results back to the GROMACS crew.
+
--- /dev/null
+.TH xpm2ps 1 "Tue 15 May 2001"
+.SH NAME
+xpm2ps
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3xpm2ps\fP
+.BI "-f" " root.xpm "
+.BI "-f2" " root2.xpm "
+.BI "-di" " ps.m2p "
+.BI "-do" " out.m2p "
+.BI "-o" " plot.eps "
+.BI "-xpm" " root.xpm "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-[no]w" ""
+.BI "-[no]frame" ""
+.BI "-title" " enum "
+.BI "-legend" " enum "
+.BI "-diag" " enum "
+.BI "-bx" " real "
+.BI "-by" " real "
+.BI "-rainbow" " enum "
+.BI "-skip" " int "
+.BI "-[no]zeroline" ""
+.SH DESCRIPTION
+xpm2ps makes a beautiful color plot of an XPixelMap file.
+Labels and axis can be displayed, when they are supplied
+in the correct matrix format.
+Matrix data may be generated by programs such as do_dssp, g_rms or
+g_mdmat.
+
+
+Parameters are set in the
+.B m2p
+file optionally supplied with
+
+.B -di
+. Reasonable defaults are provided. Settings for the y-axis
+default to those for the x-axis. Font names have a defaulting hierarchy:
+titlefont - legendfont; titlefont - (xfont - yfont - ytickfont)
+- xtickfont, e.g. setting titlefont sets all fonts, setting xfont
+sets yfont, ytickfont and xtickfont.
+
+
+With
+.B -f2
+a 2nd matrix file can be supplied, both matrix
+files will be read simultaneously and the upper left half of the
+first one (
+.B -f
+) is plotted together with the lower right
+half of the second one (
+.B -f2
+). The diagonal will contain
+values from the matrix file selected with
+.B -diag
+.
+Plotting of the diagonal values can be suppressed altogether by
+setting
+.B -diag
+to
+.B none
+.
+
+
+If the color coding and legend labels of both matrices are identical,
+only one legend will be displayed, else two separate legends are
+displayed.
+
+
+
+.B -title
+can be set to
+.B none
+to suppress the title, or to
+
+.B ylabel
+to show the title in the Y-label position (alongside
+the Y-axis).
+
+
+With the
+.B -rainbow
+option dull grey-scale matrices can be turned
+into attractive color pictures.
+
+
+Merged or rainbowed matrices can be written to an XPixelMap file with
+the
+.B -xpm
+option.
+.SH FILES
+.BI "-f" " root.xpm"
+.B Input
+ X PixMap compatible matrix file
+
+.BI "-f2" " root2.xpm"
+.B Input, Opt.
+ X PixMap compatible matrix file
+
+.BI "-di" " ps.m2p"
+.B Input, Opt., Lib.
+ Input file for mat2ps
+
+.BI "-do" " out.m2p"
+.B Output, Opt.
+ Input file for mat2ps
+
+.BI "-o" " plot.eps"
+.B Output, Opt.
+ Encapsulated PostScript (tm) file
+
+.BI "-xpm" " root.xpm"
+.B Output, Opt.
+ X PixMap compatible matrix file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 0"
+ Set the nicelevel
+
+.BI "-[no]w" " no"
+ View output xvg, xpm, eps and pdb files
+
+.BI "-[no]frame" " yes"
+ Display frame, ticks, labels, title and legend
+
+.BI "-title" " enum" " top"
+ Show title at: top, ylabel or none
+
+.BI "-legend" " enum" " both"
+ Show legend: both, first, second or none
+
+.BI "-diag" " enum" " first"
+ Diagonal: first, second or none
+
+.BI "-bx" " real" " 0"
+ Box x-size (also y-size when -by is not set)
+
+.BI "-by" " real" " 0"
+ Box y-size
+
+.BI "-rainbow" " enum" " no"
+ Rainbow colors, convert white to: no, blue or red
+
+.BI "-skip" " int" " 1"
+ only write out every nr-th row and column
+
+.BI "-[no]zeroline" " no"
+ insert line in xpm matrix where axis label is zero
+
--- /dev/null
+.TH xrama 1 "Tue 15 May 2001"
+.SH NAME
+xrama
+.B VERSION 3.0
+.SH SYNOPSIS
+\f3xrama\fP
+.BI "-f" " traj.xtc "
+.BI "-s" " topol.tpr "
+.BI "-[no]h" ""
+.BI "-[no]X" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.SH DESCRIPTION
+xrama shows a Ramachandran movie, that is, it shows
+the Phi/Psi angles as a function of time in an X-Window.
+
+Static Phi/Psi plots for printing can be made with g_rama.
+
+
+Some of the more common X command line options can be used:
+
+-bg, -fg change colors, -font fontname, changes the font.
+.SH FILES
+.BI "-f" " traj.xtc"
+.B Input
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-s" " topol.tpr"
+.B Input
+ Generic run input: tpr tpb tpa
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-[no]X" " no"
+ Use dialog box GUI to edit command line options
+
+.BI "-nice" " int" " 0"
+ Set the nicelevel
+
+.BI "-b" " time" " -1"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " -1"
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " -1"
+ Only use frame when t MOD dt = first time (ps)
+
htmldir = ${prefix}/html
-html_DATA = gmxfaq.html online.html style.css
+html_DATA = online.html
EXTRA_DIST = ${html_DATA}
charts_up.gif flow_leftright.gif \
flow_uprightleft.gif software.gif \
faq.gif flow_leftrightdown.gif \
- flow_vline.gif topologies.gif
+ flow_vline.gif topologies.gif \
+ plotje.gif xvgr.gif
EXTRA_DIST = ${gif_DATA}
<HTML>
-<TITLE>GROMACS 3.0 Manual </TITLE>
-<BODY text="#000000" bgcolor="#FFFFFF">
-<H1>GROMACS 3.0 manual</H1>
+<TITLE>GROMACS 3.0 Online Reference </TITLE>
+<LINK rel=stylesheet href="online/style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>GROMACS 3.0 Online Reference</H2>
+<HR>
+<P>
<TABLE BORDER=0 CELLSPACING=0 CELLPADDING=10>
<TR>
<TD VALIGN=top WIDTH="25%">
<h3>General</h3>
-<A HREF="changes3.0.html">New features</a>
+<A HREF="online/getting_started.html">Getting Started</a>
+<br><br>
+<A HREF="online/flow.html">Flow Chart</a>
+<br><br>
+<A HREF="online/files.html">File Formats</a>
+<br><br>
+<A HREF="online/mdp_opt.html">mdp options</a>
+<br><br>
+<A HREF="gmxfaq.html">FAQ</a>
<br>
-<br><A HREF="online/getting_started.html">Getting Started</a>
-<br>
-<br><A HREF="online/flow.html" >Flow chart</a>
-<br>
-<br><A HREF="online/files.html" >File formats</a>
-<br>
-<br><A HREF="online/mdp_opt.html" >mdp options</a>
+<br><A HREF="http://www.gromacs.org">GROMACS homepage</A>
</TD>
-<TD VALIGN=top WIDTH="75%">
+<TD VALIGN=top WIDTH=75%>
<h3>Programs</h3>
<multicol cols=5>
-<A HREF="online/options.html" >Options</a>
+<A HREF="online/options.html">Options</a>
<br>
-<br><a href="online/average.html">average</a>
-<br><a href="online/do_dssp.html">do_dssp</a>
-<br><a href="online/editconf.html">editconf</a>
-<br><a href="online/eneconv.html">eneconv</a>
-<br><a href="online/g_anaeig.html">g_anaeig</a>
-<br><a href="online/g_analyze.html">g_analyze</a>
-<br><a href="online/g_angle.html">g_angle</a>
-<br><a href="online/g_bond.html">g_bond</a>
-<br><a href="online/g_bundle.html">g_bundle</a>
-<br><a href="online/g_chi.html">g_chi</a>
-<br><a href="online/g_cluster.html">g_cluster</a>
-<br><a href="online/g_confrms.html">g_confrms</a>
-<br><a href="online/g_covar.html">g_covar</a>
-<br><a href="online/g_density.html">g_density</a>
-<br><a href="online/g_dielectric.html">g_dielectric</a>
-<br><a href="online/g_dih.html">g_dih</a>
-<br><a href="online/g_dipoles.html">g_dipoles</a>
-<br><a href="online/g_disre.html">g_disre</a>
-<br><a href="online/g_dist.html">g_dist</a>
-<br><a href="online/g_dyndom.html">g_dyndom</a>
-<br><a href="online/genbox.html">genbox</a>
-<br><a href="online/genconf.html">genconf</a>
-<br><a href="online/g_enemat.html">g_enemat</a>
-<br><a href="online/g_energy.html">g_energy</a>
-<br><a href="online/genion.html">genion</a>
-<br><a href="online/genpr.html">genpr</a>
-<br><a href="online/g_gyrate.html">g_gyrate</a>
-<br><a href="online/g_h2order.html">g_h2order</a>
-<br><a href="online/g_hbond.html">g_hbond</a>
-<br><a href="online/g_helix.html">g_helix</a>
-<br><a href="online/g_lie.html">g_lie</a>
-<br><a href="online/g_mdmat.html">g_mdmat</a>
-<br><a href="online/g_mindist.html">g_mindist</a>
-<br><a href="online/g_morph.html">g_morph</a>
-<br><a href="online/g_msd.html">g_msd</a>
-<br><a href="online/gmxcheck.html">gmxcheck</a>
-<br><a href="online/gmxdump.html">gmxdump</a>
-<br><a href="online/g_nmeig.html">g_nmeig</a>
-<br><a href="online/g_nmens.html">g_nmens</a>
-<br><a href="online/g_order.html">g_order</a>
-<br><a href="online/g_potential.html">g_potential</a>
-<br><a href="online/g_rama.html">g_rama</a>
-<br><a href="online/g_rdf.html">g_rdf</a>
-<br><a href="online/g_rms.html">g_rms</a>
-<br><a href="online/g_rmsdist.html">g_rmsdist</a>
-<br><a href="online/g_rmsf.html">g_rmsf</a>
-<br><a href="online/grompp.html">grompp</a>
-<br><a href="online/g_rotacf.html">g_rotacf</a>
-<br><a href="online/g_saltbr.html">g_saltbr</a>
-<br><a href="online/g_sas.html">g_sas</a>
-<br><a href="online/g_sgangle.html">g_sgangle</a>
-<br><a href="online/g_sorient.html">g_sorient</a>
-<br><a href="online/g_tcaf.html">g_tcaf</a>
-<br><a href="online/g_traj.html">g_traj</a>
-<br><a href="online/g_velacc.html">g_velacc</a>
-<br><a href="online/highway.html">highway</a>
-<br><a href="online/make_ndx.html">make_ndx</a>
-<br><a href="online/mdrun.html">mdrun</a>
-<br><a href="online/mk_angndx.html">mk_angndx</a>
-<br><a href="online/ngmx.html">ngmx</a>
-<br><a href="online/nmrun.html">nmrun</a>
-<br><a href="online/pdb2gmx.html">pdb2gmx</a>
-<br><a href="online/protonate.html">protonate</a>
-<br><a href="online/tpbconv.html">tpbconv</a>
-<br><a href="online/trjcat.html">trjcat</a>
-<br><a href="online/trjconv.html">trjconv</a>
-<br><a href="online/trjorder.html">trjorder</a>
-<br><a href="online/wheel.html">wheel</a>
-<br><a href="online/x2top.html">x2top</a>
-<br><a href="online/xpm2ps.html">xpm2ps</a>
-<br><a href="online/xrama.html">xrama</a>
+<br><a href=online/average.html>average</a>
+<br><a href=online/do_dssp.html>do_dssp</a>
+<br><a href=online/editconf.html>editconf</a>
+<br><a href=online/eneconv.html>eneconv</a>
+<br><a href=online/g_anaeig.html>g_anaeig</a>
+<br><a href=online/g_analyze.html>g_analyze</a>
+<br><a href=online/g_angle.html>g_angle</a>
+<br><a href=online/g_bond.html>g_bond</a>
+<br><a href=online/g_bundle.html>g_bundle</a>
+<br><a href=online/g_chi.html>g_chi</a>
+<br><a href=online/g_cluster.html>g_cluster</a>
+<br><a href=online/g_confrms.html>g_confrms</a>
+<br><a href=online/g_covar.html>g_covar</a>
+<br><a href=online/g_density.html>g_density</a>
+<br><a href=online/g_dielectric.html>g_dielectric</a>
+<br><a href=online/g_dih.html>g_dih</a>
+<br><a href=online/g_dipoles.html>g_dipoles</a>
+<br><a href=online/g_disre.html>g_disre</a>
+<br><a href=online/g_dist.html>g_dist</a>
+<br><a href=online/g_dyndom.html>g_dyndom</a>
+<br><a href=online/genbox.html>genbox</a>
+<br><a href=online/genconf.html>genconf</a>
+<br><a href=online/g_enemat.html>g_enemat</a>
+<br><a href=online/g_energy.html>g_energy</a>
+<br><a href=online/genion.html>genion</a>
+<br><a href=online/genpr.html>genpr</a>
+<br><a href=online/g_gyrate.html>g_gyrate</a>
+<br><a href=online/g_h2order.html>g_h2order</a>
+<br><a href=online/g_hbond.html>g_hbond</a>
+<br><a href=online/g_helix.html>g_helix</a>
+<br><a href=online/g_lie.html>g_lie</a>
+<br><a href=online/g_mdmat.html>g_mdmat</a>
+<br><a href=online/g_mindist.html>g_mindist</a>
+<br><a href=online/g_morph.html>g_morph</a>
+<br><a href=online/g_msd.html>g_msd</a>
+<br><a href=online/gmxcheck.html>gmxcheck</a>
+<br><a href=online/gmxdump.html>gmxdump</a>
+<br><a href=online/g_nmeig.html>g_nmeig</a>
+<br><a href=online/g_nmens.html>g_nmens</a>
+<br><a href=online/g_order.html>g_order</a>
+<br><a href=online/g_potential.html>g_potential</a>
+<br><a href=online/g_rama.html>g_rama</a>
+<br><a href=online/g_rdf.html>g_rdf</a>
+<br><a href=online/g_rms.html>g_rms</a>
+<br><a href=online/g_rmsdist.html>g_rmsdist</a>
+<br><a href=online/g_rmsf.html>g_rmsf</a>
+<br><a href=online/grompp.html>grompp</a>
+<br><a href=online/g_rotacf.html>g_rotacf</a>
+<br><a href=online/g_saltbr.html>g_saltbr</a>
+<br><a href=online/g_sas.html>g_sas</a>
+<br><a href=online/g_sgangle.html>g_sgangle</a>
+<br><a href=online/g_sorient.html>g_sorient</a>
+<br><a href=online/g_tcaf.html>g_tcaf</a>
+<br><a href=online/g_traj.html>g_traj</a>
+<br><a href=online/g_velacc.html>g_velacc</a>
+<br><a href=online/highway.html>highway</a>
+<br><a href=online/luck.html>luck</a>
+<br><a href=online/make_ndx.html>make_ndx</a>
+<br><a href=online/mdrun.html>mdrun</a>
+<br><a href=online/mk_angndx.html>mk_angndx</a>
+<br><a href=online/ngmx.html>ngmx</a>
+<br><a href=online/nmrun.html>nmrun</a>
+<br><a href=online/pdb2gmx.html>pdb2gmx</a>
+<br><a href=online/protonate.html>protonate</a>
+<br><a href=online/tpbconv.html>tpbconv</a>
+<br><a href=online/trjcat.html>trjcat</a>
+<br><a href=online/trjconv.html>trjconv</a>
+<br><a href=online/trjorder.html>trjorder</a>
+<br><a href=online/wheel.html>wheel</a>
+<br><a href=online/x2top.html>x2top</a>
+<br><a href=online/xpm2ps.html>xpm2ps</a>
+<br><a href=online/xrama.html>xrama</a>
</multicol>
</TD>
</TR>
</TABLE>
-</BODY>
-</HTML>
+<HR>
+<h3>Programs by Topic</h3>
+<multicol cols=3>
+<A HREF="#HNR1">Generating topologies and coordinates</A><br>
+<A HREF="#HNR2">Running a simulation</A><br>
+<A HREF="#HNR3">Viewing trajectories</A><br>
+<A HREF="#HNR4">Processing energies</A><br>
+<A HREF="#HNR5">Converting files</A><br>
+<A HREF="#HNR6">Tools</A><br>
+<A HREF="#HNR7">Distances between structures</A><br>
+<A HREF="#HNR8">Distances in structures over time</A><br>
+<A HREF="#HNR9">Mass distribution properties over time</A><br>
+<A HREF="#HNR10">Analyzing bonded interactions</A><br>
+<A HREF="#HNR11">Structural properties</A><br>
+<A HREF="#HNR12">Kinetic properties</A><br>
+<A HREF="#HNR13">Electrostatic properties</A><br>
+<A HREF="#HNR14">Protein specific analysis</A><br>
+<A HREF="#HNR15">Interfaces</A><br>
+<A HREF="#HNR16">Covariance analysis</A><br>
+<A HREF="#HNR17">Normal modes</A><br>
+</multicol>
+
+<A NAME="HNR1">
+<TABLE CELLSPACING=1>
+<TR><TD>
+<TR><TD COLSPAN=2><b>Generating topologies and coordinates</b>
+<TR><TD><A HREF="online/pdb2gmx.html">pdb2gmx</A><TD>converts pdb files to topology and coordinate files
+<TR><TD><A HREF="online/x2top.html">x2top</A><TD>generates a primitive topology from coordinates
+<TR><TD><A HREF="online/editconf.html">editconf</A><TD>edits the box and writes subgroups
+<TR><TD><A HREF="online/genbox.html">genbox</A><TD>solvates a system
+<TR><TD><A HREF="online/genion.html">genion</A><TD>generates mono atomic ions on energetically favorable positions
+<TR><TD><A HREF="online/genconf.html">genconf</A><TD>multiplies a conformation in 'random' orientations
+<TR><TD><A HREF="online/genpr.html">genpr</A><TD>generates position restraints for index groups
+<TR><TD><A HREF="online/protonate.html">protonate</A><TD>protonates structures
+</TABLE>
+
+<A NAME="HNR2">
+<TABLE CELLSPACING=1>
+<TR><TD>
+<TR><TD COLSPAN=2><b>Running a simulation</b>
+<TR><TD><A HREF="online/grompp.html">grompp</A><TD>makes a run input file
+<TR><TD><A HREF="online/tpbconv.html">tpbconv</A><TD>makes a run input file for restarting a crashed run
+<TR><TD><A HREF="online/mdrun.html">mdrun</A><TD>performs a simulation
+</TABLE>
+
+<A NAME="HNR3">
+<TABLE CELLSPACING=1>
+<TR><TD>
+<TR><TD COLSPAN=2><b>Viewing trajectories</b>
+<TR><TD><A HREF="online/ngmx.html">ngmx</A><TD>displays a trajectory
+<TR><TD><A HREF="online/trjconv.html">trjconv</A><TD>converts trajectories to e.g. pdb which can be viewed with e.g. rasmol
+</TABLE>
+
+<A NAME="HNR4">
+<TABLE CELLSPACING=1>
+<TR><TD>
+<TR><TD COLSPAN=2><b>Processing energies</b>
+<TR><TD><A HREF="online/g_energy.html">g_energy</A><TD>writes energies to xvg files and displays averages
+<TR><TD><A HREF="online/g_enemat.html">g_enemat</A><TD>extracts an energy matrix from an energy file
+<TR><TD><A HREF="online/mdrun.html">mdrun</A><TD>with -rerun (re)calculates energies for trajectory frames
+</TABLE>
+
+<A NAME="HNR5">
+<TABLE CELLSPACING=1>
+<TR><TD>
+<TR><TD COLSPAN=2><b>Converting files</b>
+<TR><TD><A HREF="online/editconf.html">editconf</A><TD>converts and manipulates structure files
+<TR><TD><A HREF="online/trjconv.html">trjconv</A><TD>converts and manipulates trajectory files
+<TR><TD><A HREF="online/trjcat.html">trjcat</A><TD>concatenates trajectory files
+<TR><TD><A HREF="online/eneconv.html">eneconv</A><TD>converts energy files
+<TR><TD><A HREF="online/xmp2ps.html">xmp2ps</A><TD>converts XPM matrices to encapsulated postscript (or XPM)
+</TABLE>
+
+<A NAME="HNR6">
+<TABLE CELLSPACING=1>
+<TR><TD>
+<TR><TD COLSPAN=2><b>Tools</b>
+<TR><TD><A HREF="online/make_ndx.html">make_ndx</A><TD>makes index files
+<TR><TD><A HREF="online/mk_angndx.html">mk_angndx</A><TD>generates index files for g_angle
+<TR><TD><A HREF="online/gmxcheck.html">gmxcheck</A><TD>checks and compares files
+<TR><TD><A HREF="online/gmxdump.html">gmxdump</A><TD>makes binary files human readable
+<TR><TD><A HREF="online/g_traj.html">g_traj</A><TD>plots x, v and f of selected atoms/groups (and more) from a trajectory
+<TR><TD><A HREF="online/g_analyze.html">g_analyze</A><TD>analyzes data sets
+<TR><TD><A HREF="online/trjorder.html">trjorder</A><TD>orders molecules according to their distance to a group
+</TABLE>
+
+<A NAME="HNR7">
+<TABLE CELLSPACING=1>
+<TR><TD>
+<TR><TD COLSPAN=2><b>Distances between structures</b>
+<TR><TD><A HREF="online/g_rms.html">g_rms</A><TD>calculates rmsd's with a reference structure and rmsd matrices
+<TR><TD><A HREF="online/g_confrms.html">g_confrms</A><TD>fits two structures and calculates the rmsd
+<TR><TD><A HREF="online/g_cluster.html">g_cluster</A><TD>clusters structures
+<TR><TD><A HREF="online/g_rmsf.html">g_rmsf</A><TD>calculates atomic fluctuations
+</TABLE>
+
+<A NAME="HNR8">
+<TABLE CELLSPACING=1>
+<TR><TD>
+<TR><TD COLSPAN=2><b>Distances in structures over time</b>
+<TR><TD><A HREF="online/g_mindist.html">g_mindist</A><TD>calculates the minimum distance between two groups
+<TR><TD><A HREF="online/g_dist.html">g_dist</A><TD>calculates the distances between the centers of mass of two groups
+<TR><TD><A HREF="online/g_mdmat.html">g_mdmat</A><TD>calculates residue contact maps
+<TR><TD><A HREF="online/g_rmsdist.html">g_rmsdist</A><TD>calculates atom pair distances averaged with power 2, -3 or -6
+</TABLE>
+
+<A NAME="HNR9">
+<TABLE CELLSPACING=1>
+<TR><TD>
+<TR><TD COLSPAN=2><b>Mass distribution properties over time</b>
+<TR><TD><A HREF="online/g_traj.html">g_traj</A><TD>plots x, v, f, box, temperature and rotational energy
+<TR><TD><A HREF="online/g_gyrate.html">g_gyrate</A><TD>calculates the radius of gyration
+<TR><TD><A HREF="online/g_msd.html">g_msd</A><TD>calculates mean square displacements
+<TR><TD><A HREF="online/g_rotacf.html">g_rotacf</A><TD>calculates the rotational correlation function for molecules
+<TR><TD><A HREF="online/g_rdf.html">g_rdf</A><TD>calculates radial distribution functions
+</TABLE>
+
+<A NAME="HNR10">
+<TABLE CELLSPACING=1>
+<TR><TD>
+<TR><TD COLSPAN=2><b>Analyzing bonded interactions</b>
+<TR><TD><A HREF="online/g_bond.html">g_bond</A><TD>calculates bond length distributions
+<TR><TD><A HREF="online/mk_angndx.html">mk_angndx</A><TD>generates index files for g_angle
+<TR><TD><A HREF="online/g_angle.html">g_angle</A><TD>calculates distributions and correlations for angles and dihedrals
+<TR><TD><A HREF="online/g_dih.html">g_dih</A><TD>analyzes dihedral transitions
+</TABLE>
+
+<A NAME="HNR11">
+<TABLE CELLSPACING=1>
+<TR><TD>
+<TR><TD COLSPAN=2><b>Structural properties</b>
+<TR><TD><A HREF="online/g_hbond.html">g_hbond</A><TD>computes and analyzes hydrogen bonds
+<TR><TD><A HREF="online/g_saltbr.html">g_saltbr</A><TD>computes salt bridges
+<TR><TD><A HREF="online/g_sas.html">g_sas</A><TD>computes solvent accessible surface area
+<TR><TD><A HREF="online/g_order.html">g_order</A><TD>computes the order parameter per atom for carbon tails
+<TR><TD><A HREF="online/g_sgangle.html">g_sgangle</A><TD>computes the angle and distance between two groups
+<TR><TD><A HREF="online/g_sorient.html">g_sorient</A><TD>analyzes solvent orientation around solutes
+<TR><TD><A HREF="online/g_bundle.html">g_bundle</A><TD>analyzes bundles of axes, e.g. helices
+<TR><TD><A HREF="online/g_disre.html">g_disre</A><TD>analyzes distance restraints
+</TABLE>
+
+<A NAME="HNR12">
+<TABLE CELLSPACING=1>
+<TR><TD>
+<TR><TD COLSPAN=2><b>Kinetic properties</b>
+<TR><TD><A HREF="online/g_traj.html">g_traj</A><TD>plots x, v, f, box, temperature and rotational energy
+<TR><TD><A HREF="online/g_velacc.html">g_velacc</A><TD>calculates velocity autocorrelation functions
+<TR><TD><A HREF="online/g_tcaf.html">g_tcaf</A><TD>calculates viscosities of liquids
+</TABLE>
+
+<A NAME="HNR13">
+<TABLE CELLSPACING=1>
+<TR><TD>
+<TR><TD COLSPAN=2><b>Electrostatic properties</b>
+<TR><TD><A HREF="online/genion.html">genion</A><TD>generates mono atomic ions on energetically favorable positions
+<TR><TD><A HREF="online/g_potential.html">g_potential</A><TD>calculates the electrostatic potential across the box
+<TR><TD><A HREF="online/g_dipoles.html">g_dipoles</A><TD>computes the total dipole plus fluctuations
+<TR><TD><A HREF="online/g_dielectric.html">g_dielectric</A><TD>calculates frequency dependent dielectric constants
+</TABLE>
+
+<A NAME="HNR14">
+<TABLE CELLSPACING=1>
+<TR><TD>
+<TR><TD COLSPAN=2><b>Protein specific analysis</b>
+<TR><TD><A HREF="online/do_dssp.html">do_dssp</A><TD>assigns secondary structure and calculates solvent accessible surface area
+<TR><TD><A HREF="online/g_chi.html">g_chi</A><TD>calculates everything you want to know about chi and other dihedrals
+<TR><TD><A HREF="online/g_helix.html">g_helix</A><TD>calculates everything you want to know about helices
+<TR><TD><A HREF="online/g_rama.html">g_rama</A><TD>computes Ramachandran plots
+<TR><TD><A HREF="online/xrama.html">xrama</A><TD>shows animated Ramachandran plots
+<TR><TD><A HREF="online/wheel.html">wheel</A><TD>plots helical wheels
+</TABLE>
+
+<A NAME="HNR15">
+<TABLE CELLSPACING=1>
+<TR><TD>
+<TR><TD COLSPAN=2><b>Interfaces</b>
+<TR><TD><A HREF="online/g_potential.html">g_potential</A><TD>calculates the electrostatic potential across the box
+<TR><TD><A HREF="online/g_density.html">g_density</A><TD>calculates the density of the system
+<TR><TD><A HREF="online/g_order.html">g_order</A><TD>computes the order parameter per atom for carbon tails
+<TR><TD><A HREF="online/g_h2order.html">g_h2order</A><TD>computes the orientation of water molecules
+<TR><TD><A HREF="online/g_bundle.html">g_bundle</A><TD>analyzes bundles of axes, e.g. transmembrane helices
+</TABLE>
+
+<A NAME="HNR16">
+<TABLE CELLSPACING=1>
+<TR><TD>
+<TR><TD COLSPAN=2><b>Covariance analysis</b>
+<TR><TD><A HREF="online/g_covar.html">g_covar</A><TD>calculates and diagonalizes the covariance matrix
+<TR><TD><A HREF="online/g_anaeig.html">g_anaeig</A><TD>analyzes the eigenvectors
+</TABLE>
+
+<A NAME="HNR17">
+<TABLE CELLSPACING=1>
+<TR><TD>
+<TR><TD COLSPAN=2><b>Normal modes</b>
+<TR><TD><A HREF="online/grompp.html">grompp</A><TD>makes a run input file
+<TR><TD><A HREF="online/mdrun.html">mdrun</A><TD>finds a potential energy minimum
+<TR><TD><A HREF="online/nmrun.html">nmrun</A><TD>calculates the Hessian
+<TR><TD><A HREF="online/g_nmeig.html">g_nmeig</A><TD>diagonalizes the Hessian
+<TR><TD><A HREF="online/g_anaeig.html">g_anaeig</A><TD>analyzes the normal modes
+<TR><TD><A HREF="online/g_nmens.html">g_nmens</A><TD>generates an ensemble of structures from the normal modes
+</TABLE>
+<p>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</body>
+</html>
onlinedir = ${prefix}/html/online
online_DATA = \
- edo.html g96.html log.html \
- options.html tpa.html xvg.html \
- edr.html m2p.html getting_started.html \
- out.html tpb.html ene.html \
- gro.html map.html tpr.html \
- eps.html hat.html mdp.html \
- xtc.html top.html pdb.html \
- trj.html dat.html files.html \
- mdp_opt.html rtp.html include_bot.html \
- trr.html dlg.html flow.html \
- mtx.html tex.html include_top.html \
- xpm.html edi.html g87.html \
- itp.html ndx.html style.css
+ dat.html g_disre.html g_sorient.html ndx.html \
+ dlg.html g_dist.html g_tcaf.html ngmx.html \
+ do_dssp.html g_dyndom.html g_traj.html nmrun.html \
+ edi.html g_enemat.html g_velacc.html options.html \
+ editconf.html g_energy.html genbox.html out.html \
+ edo.html g_gyrate.html genconf.html pdb.html \
+ edr.html g_h2order.html genion.html pdb2gmx.html \
+ ene.html g_hbond.html genpr.html protonate.html \
+ eneconv.html g_helix.html getting_started.html rtp.html \
+ eps.html g_lie.html gmxcheck.html tex.html \
+ files.html g_mdmat.html gmxdump.html top.html \
+ flow.html g_mindist.html gro.html tpa.html \
+ g87.html g_morph.html grompp.html tpb.html \
+ g96.html g_msd.html hat.html tpbconv.html \
+ g_anaeig.html g_nmeig.html highway.html tpr.html \
+ g_analyze.html g_nmens.html include_bot.html trj.html \
+ g_angle.html g_order.html include_top.html trjcat.html \
+ g_bond.html g_potential.html itp.html trjconv.html \
+ g_bundle.html g_rama.html log.html trjorder.html \
+ g_chi.html g_rdf.html m2p.html trr.html \
+ g_cluster.html g_rms.html make_ndx.html wheel.html \
+ g_confrms.html g_rmsdist.html map.html x2top.html \
+ g_covar.html g_rmsf.html mdp.html xpm.html \
+ g_density.html g_rotacf.html mdp_opt.html xpm2ps.html \
+ g_dielectric.html g_saltbr.html mdrun.html xrama.html \
+ g_dih.html g_sas.html mk_angndx.html xtc.html \
+ g_dipoles.html g_sgangle.html mtx.html xvg.html \
+ style.css
+
EXTRA_DIST = ${online_DATA}
<title>dat file format</title>
-<body>
-<h1>dat file format</h1>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<h2>dat file format</h2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
Files with the dat file extension contain generic input or output.
As it is not possible
to categorise all data file formats, GROMACS has a generic file format called
dat of which no format is given.
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
</body>
<title>dlg file format</title>
-<body>
-<h1>dlg file format</h1>
-<h2>Description</h2>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<h2>dlg file format</h2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<h3>Description</h3>
The dlg file format is used as input for the <a href="ngmx.html">ngmx</a>
trajectory viewer. These files are not meant to be altered bu the end user.
-
-<h2>Sample</h2>
+<h3>Sample</h3>
<pre>
grid 39 18 {
}
</pre>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
</body>
--- /dev/null
+<TITLE>do_dssp</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>do_dssp</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+do_dssp
+reads a trajectory file and computes the secondary structure for
+each time frame
+calling the dssp program. If you do not have the dssp program,
+get it. do_dssp assumes that the dssp executable is in
+/home/mdgroup/dssp/dssp. If that is not the case, then you should
+set an environment variable <b>DSSP</b> pointing to the dssp
+executable as in: <p>
+<tt>setenv DSSP /usr/local/bin/dssp</tt><p>
+The structure assignment for each residue and time is written to an
+<tt>.<a href="xpm.html">xpm</a></tt> matrix file. This file can be visualized with for instance
+<tt>xv</tt> and can be converted to postscript with <tt><a href="xpm2ps.html">xpm2ps</a></tt>.
+The number of residues with each secondary structure type and the
+total secondary structure (<tt>-sss</tt>) count as a function of
+time are also written to file (<tt>-sc</tt>).<p>
+Solvent accessible surface (SAS) per residue can be calculated, both in
+absolute values (A^2) and in fractions of the maximal accessible
+surface of a residue. The maximal accessible surface is defined as
+the accessible surface of a residue in a chain of glycines.
+[B]Note[b] that the program <tt><a href="g_sas.html">g_sas</a></tt> can also compute SAS
+and that is more efficient.<p>
+Finally, this program can dump the secondary structure in a special file
+<tt>ssdump.<a href="dat.html">dat</a></tt> for usage in the program <tt><a href="g_chi.html">g_chi</a></tt>. Together
+these two programs can be used to analyze dihedral properties as a
+function of secondary structure type.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-ssdump</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="dat.html"> ssdump.dat</a></tt> </TD><TD> Output, Opt. </TD><TD> Generic data file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-map</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="map.html"> ss.map</a></tt> </TD><TD> Input, Lib. </TD><TD> File that maps matrix data to colors </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html"> ss.xpm</a></tt> </TD><TD> Output </TD><TD> X PixMap compatible matrix file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-sc</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> scount.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-a</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html"> area.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-ta</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> totarea.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-aa</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">averarea.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-sss</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>HEBT</tt> </TD><TD> Secondary structures for structure count </TD></TD>
+</TABLE>
+<P>
+<H3>Diagnostics</H3>
+<UL>
+<LI>The program is very slow
+</UL>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
<title>edi file format</title>
-<body>
-<h1>edi file format</h1>
-<h2>Description</h2>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<h2>edi file format</h2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<h3>Description</h3>
Files with the edi file extension contain information for <a href="mdrun.html">
mdrun</a> to run Molecular Dynamics with Essential Dynamics constraints.
These files can be generated by the program <tt>WEDSAM</tt> which uses
output from the programs in the <tt>ESSDYN</tt> menu of the
<A HREF="http://www.sander.embl-heidelberg.de/whatif/">WHAT IF</A> program.
</TD> </TR> </TABLE>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
</body>
--- /dev/null
+<TITLE>editconf</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>editconf</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+editconf converts generic structure format to <tt>.<a href="gro.html">gro</a></tt>, <tt>.<a href="g96.html">g96</a></tt>
+or <tt>.<a href="pdb.html">pdb</a></tt>.
+<p>
+The box can be modified with options <tt>-box</tt>, <tt>-d</tt> and
+<tt>-angles</tt>. Both <tt>-box</tt> and <tt>-d</tt>
+will center the system in the box.
+<p>
+Option <tt>-bt</tt> determines the box type: <tt>tric</tt> is a
+triclinic box, <tt>cubic</tt> is a cubic box, <tt>dodecahedron</tt> is
+a rhombic dodecahedron and <tt>octahedron</tt> is a truncated octahedron.
+The last two are special cases of a triclinic box.
+The length of the three box vectors of the truncated octahedron is the
+shortest distance between two opposite hexagons.
+The volume of a dodecahedron is 0.71 and that of a truncated octahedron
+is 0.77 of that of a cubic box with the same periodic image distance.
+<p>
+Option <tt>-box</tt> requires only
+one value for a cubic box, dodecahedron and a truncated octahedron.
+With <tt>-d</tt> and <tt>tric</tt> the size of the system in the x, y
+and z directions is used. With <tt>-d</tt> and <tt>cubic</tt>,
+<tt>dodecahedron</tt> or <tt>octahedron</tt> the diameter of the system
+is used, which is the largest distance between two atoms.
+<p>
+Option <tt>-angles</tt> is only meaningful with option <tt>-box</tt> and
+a triclinic box and can not be used with option <tt>-d</tt>.
+<p>
+When <tt>-n</tt> or <tt>-ndef</tt> is set, a group
+can be selected for calculating the size and the geometric center,
+otherwise the whole system is used.
+<p>
+<tt>-rotate</tt> rotates the coordinates and velocities.
+<tt>-princ</tt> aligns the principal axes of the system along the
+coordinate axes, this may allow you to decrease the box volume,
+but beware that molecules can rotate significantly in a nanosecond.<p>
+Scaling is applied before any of the other operations are
+performed. Boxes can be scaled to give a certain density (option
+<tt>-density</tt>). A special feature of the scaling option, when the
+factor -1 is given in one dimension, one obtains a mirror image,
+mirrored in one of the plains, when one uses -1 in three dimensions
+a point-mirror image is obtained.<p>
+Groups are selected after all operations have been applied.<p>
+Periodicity can be removed in a crude manner.
+It is important that the box sizes at the bottom of your input file
+are correct when the periodicity is to be removed.
+<p>
+The program can optionally rotate the solute molecule to align the
+molecule along its principal axes (<tt>-rotate</tt>)
+<p>
+When writing <tt>.<a href="pdb.html">pdb</a></tt> files, B-factors can be
+added with the <tt>-bf</tt> option. B-factors are read
+from a file with with following format: first line states number of
+entries in the file, next lines state an index
+followed by a B-factor. The B-factors will be attached per residue
+unless an index is larger than the number of residues or unless the
+<tt>-atom</tt> option is set. Obviously, any type of numeric data can
+be added instead of B-factors. <tt>-legend</tt> will produce
+a row of CA atoms with B-factors ranging from the minimum to the
+maximum value found, effectively making a legend for viewing.
+<p>
+With the option -mead a special <a href="pdb.html">pdb</a> file for the MEAD electrostatics
+program (Poisson-Boltzmann solver) can be made. A further prerequisite
+is that the input file is a run input file.
+The B-factor field is then filled with the Van der Waals radius
+of the atoms while the occupancy field will hold the charge.
+<p>
+The option -grasp is similar, but it puts the charges in the B-factor
+and the radius in the occupancy.
+<p>
+Finally with option <tt>-label</tt> editconf can add a chain identifier
+to a <a href="pdb.html">pdb</a> file, which can be useful for analysis with e.g. rasmol.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> conf.gro</a></tt> </TD><TD> Input </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> out.gro</a></tt> </TD><TD> Output </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-bf</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="dat.html"> bfact.dat</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic data file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]ndef</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Choose output from default index groups </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-bt</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>tric</tt> </TD><TD> Box type for -box and -d: tric, cubic, dodecahedron or octahedron </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-box</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 0</tt> </TD><TD> Box vector lengths (a,b,c) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-angles</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>90 90 90</tt> </TD><TD> Angles between the box vectors (bc,ac,ab) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-d</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Distance between the solute and the box </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]c</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Center molecule in box (implied by -box and -d) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-center</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 0</tt> </TD><TD> Coordinates of geometrical center </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-rotate</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 0</tt> </TD><TD> Rotation around the X, Y and Z axes in degrees </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]princ</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Orient molecule(s) along their principal axes </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-scale</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>1 1 1</tt> </TD><TD> Scaling factor </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-density</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 1000</tt> </TD><TD> Density (g/l) of the output box achieved by scaling </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Remove the periodicity (make molecule whole again) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]mead</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Store the charge of the atom in the occupancy field and the radius of the atom in the B-factor field </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]grasp</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Store the charge of the atom in the B-factor field and the radius of the atom in the occupancy field </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-rvdw</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.12</tt> </TD><TD> Default Van der Waals radius if one can not be found in the database </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]atom</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Force B-factor attachment per atom </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]legend</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Make B-factor legend </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-label</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>A</tt> </TD><TD> Add chain label for all residues </TD></TD>
+</TABLE>
+<P>
+<H3>Diagnostics</H3>
+<UL>
+<LI>For complex molecules, the periodicity removal routine may break down, in that case you can use <a href="trjconv.html">trjconv</a>
+</UL>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
<title>edo file format</title>
-<body>
-<h1>edo file format</h1>
-<h2>Description</h2>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<h2>edo file format</h2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<h3>Description</h3>
Files with the edo file extension are generated by <a href="mdrun.html">
mdrun</a> if Molecular Dynamics is performed with Essential Dynamics
constraints. Depending on the parameters set in the <a href="edi.html">
as RMSD values, or information about specific types of constraints.
Specific results can be extracted from the edo files with standard unix
utilities like <tt>awk</tt>.
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
</body>
<title>ene file format</title>
-<body>
-<h1>edr file format</h1>
-<h2>Description</h2>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<h2>edr file format</h2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<h3>Description</h3>
The edr file extension stands for portable energy file.
The energies are stored using the xdr protocol.
<p>
See also <a href="g_energy.html">g_energy</a>.
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
</body>
<title>ene file format</title>
-<body>
-<h1>ene file format</h1>
-<h2>Description</h2>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<h2>ene file format</h2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<h3>Description</h3>
The ene file extension stands for binary energy file. It holds the
energies as generated during your <a href="mdrun.html">mdrun</a>.
<br>
eneconv</a>.
<p>
See also <a href="g_energy.html">g_energy</a>.
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
</body>
--- /dev/null
+<TITLE>eneconv</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>eneconv</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+When <tt>-f</tt> is <it>not</it> specified:<br>
+Concatenates several energy files in sorted order.
+In case of double time frames the one
+in the later file is used. By specifying <tt>-settime</tt> you will be
+asked for the start time of each file. The input files are taken
+from the command line,
+such that the command <tt>eneconv -o fixed.<a href="edr.html">edr</a> *.<a href="edr.html">edr</a></tt> should do
+the trick. <p>
+With <tt>-f</tt> specified:<br>
+Reads one energy file and writes another, applying the <tt>-dt</tt>,
+<tt>-offset</tt>, <tt>-t0</tt> and <tt>-settime</tt> options and
+converting to a different format if necessary (indicated by file
+extentions).<p>
+<tt>-settime</tt> is applied first, then <tt>-dt</tt>/<tt>-offset</tt>
+followed by <tt>-b</tt> and <tt>-e</tt> to select which frames to write.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> ener.edr</a></tt> </TD><TD> Input </TD><TD> Generic energy: <a href="edr.html">edr</a> <a href="ene.html">ene</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> fixed.edr</a></tt> </TD><TD> Output, Opt. </TD><TD> Generic energy: <a href="edr.html">edr</a> <a href="ene.html">ene</a> </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First time to use </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last time to use </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only write out frame when t MOD dt = offset </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-offset</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Time offset for -dt option </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]settime</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Change starting time interactively </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]sort</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Sort energy files (not frames) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-scalefac</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 1</tt> </TD><TD> Multiply energy component by this factor </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]error</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Stop on errors in the file </TD></TD>
+</TABLE>
+<P>
+<H3>Diagnostics</H3>
+<UL>
+<LI>When combining trajectories the sigma and E^2 (necessary for statistics) are not updated correctly. Only the actual energy is correct. One thus has to compute statistics in another way.
+</UL>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
<title>eps file format</title>
-<body>
-<h1>eps file format</h1>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<h2>eps file format</h2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
The eps file format is not a special GROMACS format, but just a
variant of the standard PostScript(tm). A sample eps file as
generated by the <a href="xpm2ps.html">xpm2ps</a> program is
of time.
<p>
<img src="../gif/plotje.gif" alt="hallo">
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
</body>
<TITLE>File formats</TITLE>
-<BODY>
-
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
<h2>File formats</h2>
-<p>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
<dl>
-<dt>Parameter files:
-<dd> <dl compact>
-<dt><a href="mdp.html">mdp</a>
+<dt><h3>Parameter files</h3>
+<dl compact>
+<a href="mdp.html">mdp</a>
<dd>run parameters, input for <a href="grompp.html">grompp</a> and
<a href="tpbconv.html">tpbconv</a>
<dt><a href="m2p.html">m2p</a>
<dd>input for <a href="xpm2ps.html">xpm2ps</a>
</dl>
-<br><dt>Structure files:
+<br><dt><h3>Structure files</h3>
<dd> <dl compact>
<dt><a href="gro.html">gro</a> <dd>GROMACS format
<dt><a href="g96.html">g96</a> <dd>GROMOS-96 format
<dt><a href="pdb.html">pdb</a> <dd>brookhaven Protein DataBank format
-<dt><b>Generic structure format:</b>
+<dt><b>Generic structure formats:</b>
<a href="gro.html">gro</a>,
<a href="g96.html">g96</a>,
<a href="pdb.html">pdb</a>,
When gro or pdb is used approximate masses will be read from the mass database.
</dl>
-<br><dt>Topology files:
+<br><dt><h3>Topology files</h3>
<dd><dl compact>
<dt><a href="top.html">top</a> <dd>system topology (ascii)
<dt><a href="itp.html">itp</a> <dd>include topology (ascii)
<dt><a href="ndx.html">ndx</a> <dd>index file
</dl>
-<br><dt>Run Input files:
+<br><dt><h3>Run Input files</h3>
<dd><dl compact>
<dt><a href="tpr.html">tpr</a> <dd>system topology, parameters, coordinates
and velocities (binary, portable)
and velocities (ascii)
<dt><a href="tpb.html">tpb</a> <dd>system topology, parameters, coordinates
and velocities (binary)
-<dt><b>Generic run input file format:</b>
+<dt><b>Generic run input file formats:</b>
<a href="tpr.html">tpr</a>,
<a href="tpb.html">tpb</a> or
<a href="tpa.html">tpa</a>
</dl>
-<br><dt>Trajectory files:
+<br><dt><h3>Trajectory files</h3>
<dd><dl compact>
<dt><a href="trj.html">trj</a> <dd>x, v and f (binary, full precision)
<dt><a href="trr.html">trr</a> <dd>x, v and f (binary, full precision, portable)
<dt><a href="gro.html">gro</a> <dd>x and v (ascii, any precision)
<dt><a href="g96.html">g96</a> <dd>x only (ascii, fixed high precision)
<dt><a href="pdb.html">pdb</a> <dd>x only (ascii, reduced precision)
-<dt><b>Full precision format:</b>
+<dt><b>Full precision formats:</b>
<a href="trr.html">trr</a> or
<a href="trj.html">trj</a>
-<dt><b>Generic trajectory format:</b>
+<dt><b>Generic trajectory formats:</b>
<a href="xtc.html">xtc</a>,
<a href="trr.html">trr</a>,
<a href="trj.html">trj</a>,
<a href="g87.html">g87</a>
</dl>
-<br><dt>Energy files:
+<br><dt><h3>Energy files</h3>
<dd><dl compact>
<dt><a href="ene.html">ene</a> <dd>energies, temperature, pressure, box size,
density and virials (binary)
<dt><a href="edr.html">edr</a> <dd>energies, temperature, pressure, box size,
density and virials (binary, portable)
-<dt><b>Generic energy format:</b>
+<dt><b>Generic energy formats:</b>
<a href="edr.html">edr</a> or
<a href="ene.html">ene</a>
</dl>
-<br><dt>Other files:
+<br><dt><h3>Other files</h3>
<dd><dl compact>
<dt><a href="dat.html">dat</a> <dd>generic, preferred for input
<dt><a href="edi.html">edi</a>
<dt><a href="xvg.html">xvg</a> <dd>xvgr input
</dl>
</dl>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
</BODY>
\ No newline at end of file
GROMACS Flow Chart
</TITLE>
</HEAD>
-<BODY LINK=#0000FF TEXT=#00000 VLINK=#0000FF ALINK=#FF0000>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
<H2>GROMACS Flow chart</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
This is a flow chart of a typical GROMACS MD run of a protein
in a box of water.
A more detailed example is available in the
</CENTER>
<br>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
</BODY>
<title>Gromos87 trajectory file format</title>
-<body>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
<h2>g87 file format</h2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
This is a simple ASCII format:<br>
<pre>
TITLE
The number of atoms is <b>not</b> stored, neither is there any indication
of whether a box is present. The box is stored only for constant pressure
simulations. So, you simply have to remember this stuff.
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
</body>
<title>g96 file format</title>
-<body>
-<h1>g96 file format</h1>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<h2>g96 file format</h2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
<p>A file with the g96 extension can be a GROMOS-96 initial/final
configuration file or a coordinate trajectory file or a combination of both.
See the GROMOS-96 manual for a complete description of the blocks.
<p>
Note that all GROMACS programs can read compressed or g-zipped files.
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
</body>
--- /dev/null
+<TITLE>g_anaeig</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>g_anaeig</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+<tt>g_anaeig</tt> analyzes eigenvectors. The eigenvectors can be of a
+covariance matrix (<tt><a href="g_covar.html">g_covar</a></tt>) or of a Normal Modes anaysis
+(<tt><a href="g_nmeig.html">g_nmeig</a></tt>).<p>
+When a trajectory is projected on eigenvectors, all structures are
+fitted to the structure in the eigenvector file, if present, otherwise
+to the structure in the structure file. When no run input file is
+supplied, periodicity will not be taken into account. Most analyses
+are performed on eigenvectors <tt>-first</tt> to <tt>-last</tt>, but when
+<tt>-first</tt> is set to -1 you will be prompted for a selection.<p>
+<tt>-disp</tt>: plot all atom displacements of eigenvectors
+<tt>-first</tt> to <tt>-last</tt>.<p>
+<tt>-proj</tt>: calculate projections of a trajectory on eigenvectors
+<tt>-first</tt> to <tt>-last</tt>.
+The projections of a trajectory on the eigenvectors of its
+covariance matrix are called principal components (pc's).
+It is often useful to check the cosine content the pc's,
+since the pc's of random diffusion are cosines with the number
+of periods equal to half the pc index.
+The cosine content of the pc's can be calculated with the program
+<tt><a href="g_analyze.html">g_analyze</a></tt>.<p>
+<tt>-2d</tt>: calculate a 2d projection of a trajectory on eigenvectors
+<tt>-first</tt> and <tt>-last</tt>.<p>
+<tt>-3d</tt>: calculate a 3d projection of a trajectory on the first
+three selected eigenvectors.<p>
+<tt>-filt</tt>: filter the trajectory to show only the motion along
+eigenvectors <tt>-first</tt> to <tt>-last</tt>.<p>
+<tt>-extr</tt>: calculate the two extreme projections along a trajectory
+on the average structure and interpolate <tt>-nframes</tt> frames
+between them, or set your own extremes with <tt>-max</tt>. The
+eigenvector <tt>-first</tt> will be written unless <tt>-first</tt> and
+<tt>-last</tt> have been set explicitly, in which case all eigenvectors
+will be written to separate files. Chain identifiers will be added
+when writing a <tt>.<a href="pdb.html">pdb</a></tt> file with two or three structures (you
+can use <tt>rasmol -nmrpdb</tt> to view such a <a href="pdb.html">pdb</a> file).<p>
+ Overlap calculations between covariance analysis:<br>
+ NOTE: the analysis should use the same fitting structure<p>
+<tt>-over</tt>: calculate the subspace overlap of the eigenvectors in
+file <tt>-v2</tt> with eigenvectors <tt>-first</tt> to <tt>-last</tt>
+in file <tt>-v</tt>.<p>
+<tt>-inpr</tt>: calculate a matrix of inner-products between
+eigenvectors in files <tt>-v</tt> and <tt>-v2</tt>. All eigenvectors
+of both files will be used unless <tt>-first</tt> and <tt>-last</tt>
+have been set explicitly.<p>
+When <tt>-v</tt>, <tt>-eig1</tt>, <tt>-v2</tt> and <tt>-eig2</tt> are given,
+a single number for the overlap between the covariance matrices is
+generated. The formulas are:<br>
+ difference = sqrt(tr((sqrt(M1) - sqrt(M2))^2))<br>
+normalized overlap = 1 - difference/sqrt(tr(M1) + tr(M2))<br>
+ shape overlap = 1 - sqrt(tr((sqrt(M1/tr(M1)) - sqrt(M2/tr(M2)))^2))<br>
+where M1 and M2 are the two covariance matrices and tr is the trace
+of a matrix. The numbers are proportional to the overlap of the square
+root of the fluctuations. The normalized overlap is the most useful
+number, it is 1 for identical matrices and 0 when the sampled
+subspaces are orthogonal.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-v</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">eigenvec.trr</a></tt> </TD><TD> Input </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-v2</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">eigenvec2.trr</a></tt> </TD><TD> Input, Opt. </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input, Opt. </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-eig1</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">eigenval1.xvg</a></tt> </TD><TD> Input, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-eig2</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">eigenval2.xvg</a></tt> </TD><TD> Input, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-disp</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> eigdisp.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-proj</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> proj.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-2d</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> 2dproj.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-3d</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> 3dproj.pdb</a></tt> </TD><TD> Output, Opt. </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-filt</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">filtered.xtc</a></tt> </TD><TD> Output, Opt. </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-extr</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> extreme.pdb</a></tt> </TD><TD> Output, Opt. </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-over</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> overlap.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-inpr</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html"> inprod.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: ps, fs, ns, us, ms, s, m or h </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-first</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> First eigenvector for analysis (-1 is select) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-last</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>8</tt> </TD><TD> Last eigenvector for analysis (-1 is till the last) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-skip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Only analyse every nr-th frame </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-max</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Maximum for projection of the eigenvector on the average structure, max=0 gives the extremes </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nframes</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>2</tt> </TD><TD> Number of frames for the extremes output </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]split</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Split eigenvector projections where time is zero </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>g_analyze</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>g_analyze</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+g_analyze reads an ascii file and analyzes data sets.
+A line in the input file may start with a time
+(see option <tt>-time</tt>) and any number of y values may follow.
+Multiple sets can also be
+read when they are seperated by & (option <tt>-n</tt>),
+in this case only one y value is read from each line.
+All lines starting with # and @ are skipped.
+All analyses can also be done for the derivative of a set
+(option <tt>-d</tt>).<p>
+All options, except for <tt>-av</tt> and <tt>-power</tt> assume that the
+points are equidistant in time.<p>
+g_analyze always shows the average and standard deviation of each
+set. For each set it also shows the relative deviation of the third
+and forth cumulant from those of a Gaussian distribution with the same
+standard deviation.<p>
+Option <tt>-ac</tt> produces the autocorrelation function(s).<p>
+Option <tt>-cc</tt> plots the resemblance of set i with a cosine of
+i/2 periods. The formula is:<br>2 (int0-T y(t) cos(pi t/i) dt)^2 / int0-T y(t) y(t) dt<br>
+This is useful for principal components obtained from covariance
+analysis, since the principal components of random diffusion are
+pure cosines.<p>
+Option <tt>-msd</tt> produces the mean square displacement(s).<p>
+Option <tt>-dist</tt> produces distribution plot(s).<p>
+Option <tt>-av</tt> produces the average over the sets.
+Error bars can be added with the option <tt>-errbar</tt>.
+The errorbars can represent the standard deviation, the error
+(assuming the points are independent) or the interval containing
+90% of the points, by discarding 5% of the points at the <a href="top.html">top</a> and
+the bottom.<p>
+Option <tt>-ee</tt> produces error estimates using block averaging.
+A set is divided in a number of blocks and averages are calculated for
+each block. The error for the total average is calculated from
+the variance between averages of the m blocks B_i as follows:
+error^2 = Sum (B_i - <B>)^2 / (m*(m-1)).
+These errors are plotted as a function of the block size.
+Also an analytical block average curve is plotted, assuming
+that the autocorrelation is a sum of two exponentials.
+The analytical curve for the block average BA is:<br>
+BA(t) = sigma sqrt(2/T ( a (tau1 ((exp(-t/tau1) - 1) tau1/t + 1)) +<br>
+ (1-a) (tau2 ((exp(-t/tau2) - 1) tau2/t + 1)))),<br>where T is the total time.
+a, tau1 and tau2 are obtained by fitting BA(t) to the calculated block
+average.
+When the actual block average is very close to the analytical curve,
+the error is sigma*sqrt(2/T (a tau1 + (1-a) tau2)).<p>
+Option <tt>-power</tt> fits the data to b t^a, which is accomplished
+by fitting to a t + b on log-log scale. All points after the first
+zero or negative value are ignored.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> graph.xvg</a></tt> </TD><TD> Input </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-ac</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">autocorr.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-msd</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> msd.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-cc</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> coscont.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-dist</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> distr.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-av</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> average.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-ee</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> errest.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]time</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Expect a time in the input </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First time to read from set </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last time to read from set </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Read # sets seperated by & </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]d</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use the derivative </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-bw</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.1</tt> </TD><TD> Binwidth for the distribution </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-errbar</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Error bars for -av: none, stddev, error or 90 </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]power</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Fit data to: b t^a </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]subav</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Subtract the average before autocorrelating </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]oneacf</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Calculate one ACF over all sets </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-acflen</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Length of the ACF, default is half the number of frames </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Normalize ACF </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-P</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or 3 </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: none, exp, aexp, exp_exp or vac </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ncskip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip N points in the output file of correlation functions </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-beginfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Time where to begin the exponential fit of the correlation function </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-endfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Time where to end the exponential fit of the correlation function, -1 is till the end </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>g_angle</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>g_angle</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+g_angle computes the angle distribution for a number of angles
+or dihedrals. This way you can check whether your simulation
+is correct. With option -ov you can plot the average angle of
+a group of angles as a function of time. With the -all option
+the first graph is the average, the rest are the individual angles.<p>
+With the -of option g_angle also calculates the fraction of trans
+dihedrals (only for dihedrals) as function of time, but this is
+probably only fun for a selected few.<p>
+With option -oc a dihedral correlation function is calculated.<p>
+It should be noted that the indexfile should contain
+atom-triples for angles or atom-quadruplets for dihedrals.
+If this is not the case, the program will crash.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> angle.ndx</a></tt> </TD><TD> Input </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-od</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> angdist.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-ov</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> angaver.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-of</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> dihfrac.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-ot</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">dihtrans.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-oh</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> trhisto.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-oc</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> dihcorr.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-type</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>angle</tt> </TD><TD> Type of angle to analyse: angle, dihedral, improper or ryckaert-bellemans </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]all</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Plot all angles separately in the averages file, in the order of appearance in the index file. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-binwidth</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 1</tt> </TD><TD> binwidth (degrees) for calculating the distribution </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]chandler</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use Chandler correlation function (N[trans] = 1, N[gauche] = 0) rather than cosine correlation function. Trans is defined as phi < -60 || phi > 60. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]avercorr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Average the correlation functions for the individual angles/dihedrals </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-acflen</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Length of the ACF, default is half the number of frames </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Normalize ACF </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-P</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or 3 </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: none, exp, aexp, exp_exp or vac </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ncskip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip N points in the output file of correlation functions </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-beginfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Time where to begin the exponential fit of the correlation function </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-endfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Time where to end the exponential fit of the correlation function, -1 is till the end </TD></TD>
+</TABLE>
+<P>
+<H3>Diagnostics</H3>
+<UL>
+<LI>Counting transitions only works for dihedrals with multiplicity 3
+</UL>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>g_bond</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>g_bond</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+g_bond makes a distribution of bond lengths. If all is well a
+gaussian distribution should be made when using a harmonic potential.
+bonds are read from a single group in the index file in order i1-j1
+i2-j2 thru in-jn.<p>
+<tt>-tol</tt> gives the half-width of the distribution as a fraction
+of the bondlength (<tt>-blen</tt>). That means, for a bond of 0.2
+a tol of 0.1 gives a distribution from 0.18 to 0.22
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> bonds.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-l</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html"> bonds.log</a></tt> </TD><TD> Output, Opt. </TD><TD> Log file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-blen</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Bond length. By default length of first bond </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-tol</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.1</tt> </TD><TD> Half width of distribution as fraction of blen </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]aver</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Sum up distributions </TD></TD>
+</TABLE>
+<P>
+<H3>Diagnostics</H3>
+<UL>
+<LI>It should be possible to get bond information from the topology.
+</UL>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>g_bundle</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>g_bundle</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+g_bundle analyzes bundles of axes. The axes can be for instance
+helix axes. The program reads two index groups and divides both
+of them in <tt>-na</tt> parts. The groups define the tops and
+bottoms of the axes. Several quantities are written to file:
+the axis length, the distance from the axis centers to the average
+center of all axes, the total tilt, the radial tilt and the lateral
+tilt with respect to the average axis.
+<p>
+With option <tt>-oa</tt> the <a href="top.html">top</a>, mid and bottom points of each axis
+are written to a <a href="pdb.html">pdb</a> file each frame. The residue numbers correspond
+to the axis numbers. When viewing this file with <tt>rasmol</tt> use the
+command line option <tt>-nmrpdb</tt>, and type <tt>set axis true</tt> to
+display the reference axis.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-ol</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> bun_len.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-od</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">bun_dist.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-ot</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">bun_tilt.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-otr</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">bun_tiltr.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-otl</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">bun_tiltl.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-oa</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="pdb.html"> axes.pdb</a></tt> </TD><TD> Output, Opt. </TD><TD> Protein data bank file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-na</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of axes </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]z</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use the Z-axis as reference iso the average axis </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>g_chi</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>g_chi</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+g_chi computes phi, psi, omega and chi dihedrals for all your
+amino acid backbone and sidechains.
+It can compute dihedral angle as a function of time, and as
+histogram distributions.
+Output is in form of xvgr files, as well as a LaTeX table of the
+number of transitions per nanosecond.<p>
+Order parameters S2 for each of the dihedrals are calculated and
+output as xvgr file and optionally as a <a href="pdb.html">pdb</a> file with the S2
+values as B-factor.<p>
+If option <tt>-c</tt> is given, the program will
+calculate dihedral autocorrelation functions. The function used
+is C(t) = < cos(chi(tau)) cos(chi(tau+t)) >. The use of cosines
+rather than angles themselves, resolves the problem of periodicity.
+(Van der Spoel & Berendsen (1997), <b>Biophys. J. 72</b>, 2032-2041).<p>
+The option <tt>-r</tt> generates a contour plot of the average omega angle
+as a function of the phi and psi angles, that is, in a Ramachandran plot
+the average omega angle is plotted using color coding.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-c</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> conf.gro</a></tt> </TD><TD> Input </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> order.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-p</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="pdb.html"> order.pdb</a></tt> </TD><TD> Output, Opt. </TD><TD> Protein data bank file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-ss</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="dat.html"> ssdump.dat</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic data file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-jc</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">Jcoupling.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-corr</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> dihcorr.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-g</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html"> chi.log</a></tt> </TD><TD> Output </TD><TD> Log file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-r0</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> starting residue </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]phi</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Output for Phi dihedral angles </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]psi</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Output for Psi dihedral angles </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]omega</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Output for Omega dihedrals (peptide bonds) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]rama</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Generate Phi/Psi and Chi1/Chi2 ramachandran plots </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]viol</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Write a file that gives 0 or 1 for violated Ramachandran angles </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]all</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Output separate files for every dihedral. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]shift</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Compute chemical shifts from Phi/Psi angles </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-run</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> perform running average over ndeg degrees for histograms </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-maxchi</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> calculate first ndih Chi dihedrals: 0, 1, 2, 3, 4, 5 or 6 </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]normhisto</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Normalize histograms </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]ramomega</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> compute average omega as a function of phi/psi and plot it in an <a href="xpm.html">xpm</a> plot </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-bfact</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> B-factor value for <a href="pdb.html">pdb</a> file for atoms with no calculated dihedral order parameter </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-bmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Maximum B-factor on any of the atoms that make up a dihedral, for the dihedral angle to be considere in the statistics. Applies to database work where a number of X-Ray structures is analyzed. -bmax <= 0 means no limit. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-acflen</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Length of the ACF, default is half the number of frames </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Normalize ACF </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-P</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or 3 </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: none, exp, aexp, exp_exp or vac </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ncskip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip N points in the output file of correlation functions </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-beginfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Time where to begin the exponential fit of the correlation function </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-endfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Time where to end the exponential fit of the correlation function, -1 is till the end </TD></TD>
+</TABLE>
+<P>
+<H3>Diagnostics</H3>
+<UL>
+<LI>Produces MANY output files (up to about 4 times the number of residues in the protein, twice that if autocorrelation functions are calculated). Typically several hundred files are output.
+</UL>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>g_cluster</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>g_cluster</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+g_cluster can cluster structures with several different methods.
+Distances between structures can be determined from a trajectory
+or read from an XPM matrix file with the <tt>-dm</tt> option.
+RMS deviation after fitting or RMS deviation of atom-pair distances
+can be used to define the distance between structures.<p>
+full linkage: add a structure to a cluster when its distance to any
+element of the cluster is less than <tt>cutoff</tt>.<p>
+Jarvis Patrick: add a structure to a cluster when this structure
+and a structure in the cluster have each other as neighbors and
+they have a least <tt>P</tt> neighbors in common. The neighbors
+of a structure are the M closest structures or all structures within
+<tt>cutoff</tt>.<p>
+Monte Carlo: reorder the RMSD matrix using Monte Carlo.<p>
+diagonalization: diagonalize the RMSD matrix.<p>gromos: use algorithm as described in Daura <it>et al.</it>
+(<it>Angew. Chem. Int. Ed.</it> <b>1999</b>, <it>38</it>, pp 236-240).
+Count number of neighbors using cut-off, take structure with
+largest number of neighbors with all its neighbors as cluster
+and eleminate it from the pool of clusters. Repeat for remaining
+structures in pool.<p>
+When the clustering algorithm assigns each structure to exactly one
+cluster (full linkage, Jarvis Patrick and gromos) and a trajectory
+file is supplied, the structure with
+the smallest average distance to the others or the average structure
+or all structures for each cluster will be written to a trajectory
+file. When writing all structures, separate numbered files are made
+for each cluster.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input, Opt. </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-dm</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html"> rmsd.xpm</a></tt> </TD><TD> Input, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html">rmsd-clust.xpm</a></tt> </TD><TD> Output </TD><TD> X PixMap compatible matrix file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-g</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html"> cluster.log</a></tt> </TD><TD> Output </TD><TD> Log file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-dist</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">rmsd-dist.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-ev</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">rmsd-eig.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-sz</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">clust-size.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-tr</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html">clust-trans.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-ntr</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">clust-trans.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-clid</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">clust-id.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-cl</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">clusters.pdb</a></tt> </TD><TD> Output, Opt. </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: ps, fs, ns, us, ms, s, m or h </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]dista</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use RMSD of distances instead of RMS deviation </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nlevels</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>40</tt> </TD><TD> Discretize RMSD matrix in # levels </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-keepfree</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-4</tt> </TD><TD> if >0 # levels not to use when coloring clusters; if <0 nlevels/-keepfree+1 levels will not be used </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-cutoff</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.1</tt> </TD><TD> RMSD cut-off (nm) for two structures to be neighbor </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-max</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Maximum level in RMSD matrix </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-skip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Only analyze every nr-th frame </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]av</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Write average iso middle structure for each cluster </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-wcl</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Write all structures for first # clusters to numbered files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nst</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Only write all structures if more than # per cluster </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-rmsmin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> minimum rms difference with rest of cluster for writing structures </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-method</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>linkage</tt> </TD><TD> Method for cluster determination: linkage, jarvis-patrick, monte-carlo, diagonalization or gromos </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]binary</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Treat the RMSD matrix as consisting of 0 and 1, where the cut-off is given by -cutoff </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-M</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>10</tt> </TD><TD> Number of nearest neighbors considered for Jarvis-Patrick algorithm, 0 is use cutoff </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-P</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>3</tt> </TD><TD> Number of identical nearest neighbors required to form a cluster </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-seed</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1993</tt> </TD><TD> Random number seed for Monte Carlo clustering algorithm </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-niter</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>10000</tt> </TD><TD> Number of iterations for MC </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-kT</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.001</tt> </TD><TD> Boltzmann weighting factor for Monte Carlo optimization (zero turns off uphill steps) </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>g_confrms</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>g_confrms</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+g_confrms computes the root mean square deviation (RMSD) of two
+structures after LSQ fitting the second structure on the first one.
+The two structures do NOT need to have the same number of atoms,
+only the two index groups used for the fit need to be identical.
+<p>
+The superimposed structures are written to file. In a <tt>.<a href="pdb.html">pdb</a></tt> file
+the two structures will be written as separate models
+(use <tt>rasmol -nmrpdb</tt>).
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f1</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> conf1.gro</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f2</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> conf2.gro</a></tt> </TD><TD> Input </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> fit.pdb</a></tt> </TD><TD> Output </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n1</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> fit1.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n2</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> fit2.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]one</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Only write the fitted structure to file </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Try to make molecules whole again </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>g_covar</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>g_covar</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+<tt>g_covar</tt> calculates and diagonalizes the (mass-weighted)
+covariance matrix.
+All structures are fitted to the structure in the structure file.
+When this is not a run input file periodicity will not be taken into
+account. When the fit and analysis groups are identical and the analysis
+is non mass-weighted, the fit will also be non mass-weighted.<p>
+The eigenvectors are written to a trajectory file (<tt>-v</tt>).
+When the same atoms are used for the fit and the covariance analysis,
+the reference structure for the fit is written first with t=-1.
+The average (or reference when <tt>-ref</tt> is used) structure is
+written with t=0, the eigenvectors
+are written as frames with the eigenvector number as timestamp.<p>
+The eigenvectors can be analyzed with <tt><a href="g_anaeig.html">g_anaeig</a></tt>.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">eigenval.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-v</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">eigenvec.trr</a></tt> </TD><TD> Output </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-av</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> average.pdb</a></tt> </TD><TD> Output </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-l</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html"> covar.log</a></tt> </TD><TD> Output </TD><TD> Log file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]fit</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Fit to a reference structure </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]ref</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use the deviation from the conformation in the structure file instead of from the average </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]mwa</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Mass-weighted covariance analysis </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-last</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Last eigenvector to write away (-1 is till the last) </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>g_density</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>g_density</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+Compute partial densities across the box, using an index file. Densities
+in gram/cubic centimeter, number densities or electron densities can be
+calculated. For electron densities, each atom is weighed by its atomic
+partial charge.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-ei</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="dat.html">electrons.dat</a></tt> </TD><TD> Output </TD><TD> Generic data file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> density.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-d</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>Z</tt> </TD><TD> Take the normal on the membrane in direction X, Y or Z. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-sl</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>10</tt> </TD><TD> Divide the box in #nr slices. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]number</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Calculate number density instead of mass density. Hydrogens are not counted! </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]ed</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Calculate electron density instead of mass density </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]count</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Only count atoms in slices, no densities. Hydrogens are not counted </TD></TD>
+</TABLE>
+<P>
+<H3>Diagnostics</H3>
+<UL>
+<LI>When calculating electron densities, atomnames are used instead of types. This is bad.
+<LI>When calculating number densities, atoms with names that start with H are not counted. This may be surprising if you use hydrogens with names like OP3.
+</UL>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>g_dielectric</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>g_dielectric</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+dielectric calculates frequency dependent dielectric constants
+from the autocorrelation function of the total dipole moment in
+your simulation. This ACF can be generated by <a href="g_dipoles.html">g_dipoles</a>.
+For an estimate of the error you can run g_statistics on the
+ACF, and use the output thus generated for this program.
+The functional forms of the available functions are:<p>
+One parmeter : y = Exp[-a1 x]
+Two parmeters : y = a2 Exp[-a1 x]
+Three parmeter: y = a2 Exp[-a1 x] + (1 - a2) Exp[-a3 x]
+Startvalues for the fit procedure can be given on the commandline.
+It is also possible to fix parameters at their start value, use -fix
+with the number of the parameter you want to fix.
+<p>
+Three output files are generated, the first contains the ACF,
+an exponential fit to it with 1, 2 or 3 parameters, and the
+numerical derivative of the combination data/fit.
+The second file contains the real and imaginary parts of the
+frequency-dependent dielectric constant, the last gives a plot
+known as the Cole-Cole plot, in which the imaginary
+component is plotted as a function of the real component.
+For a pure exponential relaxation (Debye relaxation) the latter
+plot should be one half of a circle
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> Mtot.xvg</a></tt> </TD><TD> Input </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-d</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> deriv.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> epsw.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-c</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> cole.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]fft</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> use fast fourier transform for correlation function </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]x1</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> use first column as X axis rather than first data set </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-eint</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 5</tt> </TD><TD> Time were to end the integration of the data and start to use the fit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-bfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 5</tt> </TD><TD> Begin time of fit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-efit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 500</tt> </TD><TD> End time of fit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-tail</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 500</tt> </TD><TD> Length of function including data and tail from fit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-A</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.5</tt> </TD><TD> Start value for fit parameter A </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-tau1</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 10</tt> </TD><TD> Start value for fit parameter tau1 </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-tau2</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 1</tt> </TD><TD> Start value for fit parameter tau2 </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-eps0</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 80</tt> </TD><TD> Epsilon 0 of your liquid </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-epsRF</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 78.5</tt> </TD><TD> Epsilon of the reaction field used in your simulation. A value of 0 means infinity. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-fix</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Fix parameters at their start values, A (2), tau1 (1), or tau2 (4) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ffn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: none, exp, aexp, exp_exp or vac </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nsmooth</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>3</tt> </TD><TD> Number of points for smoothing </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>g_dih</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>g_dih</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+g_dih can do two things. The default is to analyze dihedral transitions
+by merely computing all the dihedral angles defined in your topology
+for the whole trajectory. When a dihedral flips over to another minimum
+an angle/time plot is made.<p>
+The opther option is to discretize the dihedral space into a number of
+bins, and group each conformation in dihedral space in the
+appropriate bin. The output is then given as a number of dihedral
+conformations sorted according to occupancy.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="out.html"> hello.out</a></tt> </TD><TD> Output </TD><TD> Generic output file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]sa</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Perform cluster analysis in dihedral space instead of analysing dihedral transitions. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-mult</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> mulitiplicity for dihedral angles (by default read from topology) </TD></TD>
+</TABLE>
+<P>
+<H3>Diagnostics</H3>
+<UL>
+<LI>should not ask for number of frames
+</UL>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>g_dipoles</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>g_dipoles</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+g_dipoles computes the total dipole plus fluctuations of a simulation
+system. From this you can compute e.g. the dielectric constant for
+low dielectric media<p>
+The file dip.<a href="xvg.html">xvg</a> contains the total dipole moment of a frame, the
+components as well as the norm of the vector.
+The file aver.<a href="xvg.html">xvg</a> contains < |Mu|^2 > and < |Mu| >^2 during the
+simulation.
+The file dip.<a href="xvg.html">xvg</a> contains the distribution of dipole moments during
+the simulation
+The mu_max is used as the highest value in the distribution graph.<p>
+Furthermore the dipole autocorrelation function will be computed, when
+option -c is used. It can be averaged over all molecules,
+or (with option -avercorr) it can be computed as the autocorrelation
+of the total dipole moment of the simulation box.<p>
+At the moment the dielectric constant is calculated only correct if
+a rectangular or cubic simulation box is used.<p>
+Option <tt>-g</tt> produces a plot of the distance dependent Kirkwood
+G-factor, as well as the average cosine of the angle between the dipoles
+as a function of the distance. The plot also includes gOO and hOO
+according to Nymand & Linse, JCP 112 (2000) pp 6386-6395.<p>
+<p>
+EXAMPLES<p>
+g_dipoles -P1 -n mols -o dip_sqr -mu 2.273 -mumax 5.0
+-nofft<p>
+This will calculate the autocorrelation function of the molecular
+dipoles using a first order Legendre polynomial of the angle of the
+dipole vector and itself a time t later. For this calculation 1001
+frames will be used. Further the dielectric constant will be calculated
+using an epsilonRF of infinity (default), temperature of 300 K (default) and
+an average dipole moment of the molecule of 2.273 (SPC). For the
+distribution function a maximum of 5.0 will be used.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-enx</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> ener.edr</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic energy: <a href="edr.html">edr</a> <a href="ene.html">ene</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> Mtot.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> epsilon.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-a</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> aver.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-d</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> dipdist.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-c</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> dipcorr.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-g</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> gkr.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-q</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">quadrupole.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-mu</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> dipole of a single molecule (in Debye) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-mumax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 5</tt> </TD><TD> max dipole in Debye (for histrogram) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-epsilonRF</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> epsilon of the reaction field used during the simulation, needed for dieclectric constant calculation. WARNING: 0.0 means infinity (default) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-skip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip steps in the output (but not in the computations) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-temp</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 300</tt> </TD><TD> average temperature of the simulation (needed for dielectric constant calculation) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]avercorr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> calculate AC function of average dipole moment of the simulation box rather than average of AC function per molecule </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-gkratom</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Use the n-th atom of a molecule (starting from 1) to calculate the distance between molecules rather than the center of charge (when 0) in the calculation of distance dependent Kirkwood factors </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-acflen</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Length of the ACF, default is half the number of frames </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Normalize ACF </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-P</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or 3 </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: none, exp, aexp, exp_exp or vac </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ncskip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip N points in the output file of correlation functions </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-beginfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Time where to begin the exponential fit of the correlation function </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-endfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Time where to end the exponential fit of the correlation function, -1 is till the end </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>g_disre</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>g_disre</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+g_disre computes violations of distance restraints. If necessary
+all protons can be added to a protein molecule. The program allways
+computes the instantaneous violations rather than time-averaged,
+because this analysis is done from a trajectory file afterwards
+it does not make sense to use time averaging.<p>
+An index file may be used to select specific restraints for
+printing.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-ds</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> drsum.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-da</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> draver.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-dn</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> drnum.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-dm</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> drmax.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-dr</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> restr.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-l</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html"> disres.log</a></tt> </TD><TD> Output </TD><TD> Log file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> viol.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ntop</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>6</tt> </TD><TD> Number of large violations that are stored in the log file every step </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>g_dist</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>g_dist</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+g_dist can calculate the distance between the centers of mass of two
+groups of atoms as a function of time. The total distance and its
+x, y and z components are plotted.<p>
+Or when <tt>-dist</tt> is set, print all the atoms in group 2 that are
+closer than a certain distance to the center of mass of group 1.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> dist.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dist</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Print all atoms in group 2 closer than dist to the center of mass of group 1 </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>g_dyndom</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>g_dyndom</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+g_dyndom reads a <a href="pdb.html">pdb</a> file output from DynDom
+http://md.chem.rug.nl/~steve/DynDom/dyndom.home.html
+It reads the coordinates, and the coordinates of the rotation axis
+furthermore it reads an index file containing the domains.
+Furthermore it takes the first and last atom of the arrow file
+as command line arguments (head and tail) and
+finally it takes the translation vector (given in DynDom info file)
+and the angle of rotation (also as command line arguments). If the angle
+determined by DynDom is given, one should be able to recover the
+second structure used for generating the DynDom output.
+Because of limited numerical accuracy this should be verified by
+computing an all-atom RMSD (using <tt><a href="g_confrms.html">g_confrms</a></tt>) rather than by file
+comparison (using diff).<p>
+The purpose of this program is to interpolate and extrapolate the
+rotation as found by DynDom. As a result unphysical structures with
+long or short bonds, or overlapping atoms may be produced. Visual
+inspection, and energy minimization may be necessary to
+validate the structure.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="pdb.html"> dyndom.pdb</a></tt> </TD><TD> Input </TD><TD> Protein data bank file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> rotated.xtc</a></tt> </TD><TD> Output </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> domains.ndx</a></tt> </TD><TD> Input </TD><TD> Index file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-firstangle</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Angle of rotation about rotation vector </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-lastangle</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Angle of rotation about rotation vector </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nframe</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>11</tt> </TD><TD> Number of steps on the pathway </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-maxangle</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> DymDom dtermined angle of rotation about rotation vector </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-trans</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Translation (Aangstroem) along rotation vector (see DynDom info file) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-head</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 0</tt> </TD><TD> First atom of the arrow vector </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-tail</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 0</tt> </TD><TD> Last atom of the arrow vector </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>g_enemat</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>g_enemat</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+g_enemat extracts an energy matrix from an energy file.
+With <b>-groups</b> a file must be supplied with on each
+line a group to be used. For these groups a matrices of
+interaction energies will be calculated. Also the total
+interaction energy energy per group is calculated.<p>
+An approximation of the free energy is calculated using:
+E(free) = E0 + kT log( <exp((E-E0)/kT)> ), where '<>'
+stands for time-average. A file with reference free energies
+can be supplied to calculate the free energy difference
+with some reference state. Group names (e.g. residue names
+in the reference file should correspond to the group names
+as used in the <b>-groups</b> file, but a appended number
+(e.g. residue number)in the <b>-groups</b> will be ignored
+in the comparison.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> ener.edr</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic energy: <a href="edr.html">edr</a> <a href="ene.html">ene</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-groups</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="dat.html"> groups.dat</a></tt> </TD><TD> Input </TD><TD> Generic data file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-eref</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="dat.html"> eref.dat</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic data file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-emat</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html"> emat.xpm</a></tt> </TD><TD> Output </TD><TD> X PixMap compatible matrix file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-etot</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> energy.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]sum</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Sum the energy terms selected rather than display them all </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-skip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip number of frames between data points </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]mean</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> with -groups calculates matrix of mean energies in stead of matrix for each timestep </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nlevels</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>20</tt> </TD><TD> number of levels for matrix colors </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-max</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 1e+20</tt> </TD><TD> max value for energies </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-min</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1e+20</tt> </TD><TD> min value for energies </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]coul</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> calculate Coulomb SR energies </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]coulr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> calculate Coulomb LR energies </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]coul14</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> calculate Coulomb 1-4 energies </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]lj</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> calculate Lennard-Jones SR energies </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]lj14</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> calculate Lennard-Jones 1-4 energies </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]bham</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> calculate Buckingham energies </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]free</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> calculate free energy </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-temp</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 300</tt> </TD><TD> reference temperature for free energy calculation </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>g_energy</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>g_energy</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+g_energy extracts energy components or distance restraint
+data from an energy file. The user is prompted to interactively
+select the energy terms she wants.<p>
+When the <tt>-viol</tt> option is set, the time averaged
+violations are plotted and the running time-averaged and
+instantaneous sum of violations are recalculated. Additionally
+running time-averaged and instantaneous distances between
+selected pairs can be plotted with the <tt>-pairs</tt> option.<p>
+Average and RMSD are calculated with full precision from the
+simulation (see printed manual). Drift is calculated by performing
+a LSQ fit of the data to a straight line. Total drift is drift
+multiplied by total time.<p>
+With <tt>-fee</tt> a free energy estimate is calculated using
+the formula: G = -ln < e ^ (E/kT) > * kT, where k is Boltzmann's
+constant, T is set by <tt>-fetemp</tt> and the average is over the
+ensemble (or time in a trajectory). Note that this is in principle
+only correct when averaging over the whole (Boltzmann) ensemble
+and using the potential energy. This also allows for an entropy
+estimate using G = H - T S, where H is the enthalpy (H = U + p V)
+and S entropy.<p>
+When a second energy file is specified (<tt>-f2</tt>), a free energy
+difference is calculated dF = -kT ln < e ^ -(EB-EA)/kT >A ,
+where EA and EB are the energies from the first and second energy
+files, and the average is over the ensemble A. <b>NOTE</b> that
+the energies must both be calculated from the same trajectory.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> ener.edr</a></tt> </TD><TD> Input </TD><TD> Generic energy: <a href="edr.html">edr</a> <a href="ene.html">ene</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f2</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> ener.edr</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic energy: <a href="edr.html">edr</a> <a href="ene.html">ene</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> energy.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-viol</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">violaver.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-pairs</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> pairs.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-corr</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> enecorr.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-vis</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> visco.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-ravg</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">runavgdf.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]fee</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Do a free energy estimate </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-fetemp</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 300</tt> </TD><TD> Reference temperature for free energy calculation </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-zero</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Subtract a zero-point energy </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]sum</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Sum the energy terms selected rather than display them all </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]dp</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print energies in high precision </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]mutot</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Compute the total dipole moment from the components </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-skip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip number of frames between data points </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]aver</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print also the X1,t and sigma1,t, only if only 1 energy is requested </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nmol</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Number of molecules in your sample: the energies are divided by this number </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ndf</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>3</tt> </TD><TD> Number of degrees of freedom per molecule. Necessary for calculating the heat capacity </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]fluc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Calculate autocorrelation of energy fluctuations rather than energy itself </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-acflen</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Length of the ACF, default is half the number of frames </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Normalize ACF </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-P</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or 3 </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: none, exp, aexp, exp_exp or vac </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ncskip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip N points in the output file of correlation functions </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-beginfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Time where to begin the exponential fit of the correlation function </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-endfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Time where to end the exponential fit of the correlation function, -1 is till the end </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>g_gyrate</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>g_gyrate</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+g_gyrate computes the radius of gyration of a group of atoms
+and the radii of gyration about the x, y and z axes,as a function of time. The atoms are explicitly mass weighted.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> gyrate.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]q</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use absolute value of the charge of an atom as weighting factor instead of mass </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]p</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Calculate the radii of gyration about the principal axes. </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>g_h2order</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>g_h2order</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+Compute the orientation of water molecules with respect to the normal
+of the box. The program determines the average cosine of the angle
+between de dipole moment of water and an axis of the box. The box is
+divided in slices and the average orientation per slice is printed.
+Each water molecule is assigned to a slice, per time frame, based on the
+position of the oxygen. When -nm is used the angle between the water
+dipole and the axis from the center of mass to the oxygen is calculated
+instead of the angle between the dipole and a box axis.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-nm</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> order.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-d</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>Z</tt> </TD><TD> Take the normal on the membrane in direction X, Y or Z. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-sl</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Calculate order parameter as function of boxlength, dividing the box in #nr slices. </TD></TD>
+</TABLE>
+<P>
+<H3>Diagnostics</H3>
+<UL>
+<LI>The program assigns whole water molecules to a slice, based on the firstatom of three in the index file group. It assumes an order O,H,H.Name is not important, but the order is. If this demand is not met,assigning molecules to slices is different.
+</UL>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>g_hbond</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>g_hbond</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+g_hbond computes and analyzes hydrogen bonds. Hydrogen bonds are
+determined based on cutoffs for the angle Donor - Hydrogen - Acceptor
+(zero is extended) and the distance Hydrogen - Acceptor.
+OH and NH groups are regarded as donors, O is an acceptor always,
+N is an acceptor by default, but this can be switched using
+<tt>-nitacc</tt>. Dummy hydrogen atoms are assumed to be connected
+to the first preceding non-hydrogen atom.<p>
+You need to specify two groups for analysis, which must be either
+identical or non-overlapping. All hydrogen bonds between the two
+groups are analyzed.<p>
+If you set -shell, you will be asked for an additional index group
+which should contain exactly one atom. In this case, only hydrogen
+bonds between atoms within the shell distance from the one atom are
+considered.<p>It is also possible to analyse specific hydrogen bonds with
+<tt>-sel</tt>. This index file must contain a group of atom triplets
+Donor Hydrogen Acceptor, in the following way:<p>
+<tt>
+[ selected ]<br>
+ 20 21 24<br>
+ 25 26 29<br>
+ 1 3 6<br>
+</tt><br>
+Note that the triplets need not be on separate lines.
+Each atom triplet specifies a hydrogen bond to be analyzed,
+note also that no check is made for the types of atoms.<p>
+<tt>-ins</tt> turns on computing solvent insertion into hydrogen bonds.
+In this case an additional group must be selected, specifying the
+solvent molecules.<p>
+<b>Output:</b><br>
+<tt>-num</tt>: number of hydrogen bonds as a function of time.<br>
+<tt>-ac</tt>: average over all autocorrelations of the existence
+functions (either 0 or 1) of all hydrogen bonds.<br>
+<tt>-dist</tt>: distance distribution of all hydrogen bonds.<br>
+<tt>-ang</tt>: angle distribution of all hydrogen bonds.<br>
+<tt>-hx</tt>: the number of n-n+i hydrogen bonds as a function of time
+where n and n+i stand for residue numbers and i ranges from 0 to 6.
+This includes the n-n+3, n-n+4 and n-n+5 hydrogen bonds associated
+with helices in proteins.<br>
+<tt>-hbn</tt>: all selected groups, donors, hydrogens and acceptors
+for selected groups, all hydrogen bonded atoms from all groups and
+all solvent atoms involved in insertion.<br>
+<tt>-hbm</tt>: existence matrix for all hydrogen bonds over all
+frames, this also contains information on solvent insertion
+into hydrogen bonds. Ordering is identical to that in <tt>-hbn</tt>
+index file.<br>
+<tt>-da</tt>: write out the number of donors and acceptors analyzed for
+each timeframe. This is especially usefull when using <tt>-shell</tt>.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-g</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html"> hbond.log</a></tt> </TD><TD> Output, Opt. </TD><TD> Log file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-sel</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> select.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-num</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> hbnum.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-ac</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> hbac.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-dist</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> hbdist.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-ang</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> hbang.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-hx</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> hbhelix.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-hbn</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> hbond.ndx</a></tt> </TD><TD> Output, Opt. </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-hbm</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html"> hbmap.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-da</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> danum.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]ins</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Analyze solvent insertion </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-a</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 60</tt> </TD><TD> Cutoff angle (degrees, Donor - Hydrogen - Acceptor) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-r</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.25</tt> </TD><TD> Cutoff radius (nm, Hydrogen - Acceptor) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-abin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 1</tt> </TD><TD> Binwidth angle distribution (degrees) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-rbin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.005</tt> </TD><TD> Binwidth distance distribution (nm) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]nitacc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Regard nitrogen atoms as acceptors </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-shell</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> when > 0, only calculate hydrogen bonds within # nm shell around one particle </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>g_helix</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>g_helix</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+g_helix computes all kind of helix properties. First, the peptide
+is checked to find the longest helical part. This is determined by
+Hydrogen bonds and Phi/Psi angles.
+That bit is fitted
+to an ideal helix around the Z-axis and centered around the origin.
+Then the following properties are computed:<p>
+<b>1.</b> Helix radius (file radius.<a href="xvg.html">xvg</a>). This is merely the
+RMS deviation in two dimensions for all Calpha atoms.
+it is calced as sqrt((SUM i(x^2(i)+y^2(i)))/N), where N is the number
+of backbone atoms. For an ideal helix the radius is 0.23 nm<br>
+<b>2.</b> Twist (file twist.<a href="xvg.html">xvg</a>). The average helical angle per
+residue is calculated. For alpha helix it is 100 degrees,
+for 3-10 helices it will be smaller,
+for 5-helices it will be larger.<br>
+<b>3.</b> Rise per residue (file rise.<a href="xvg.html">xvg</a>). The helical rise per
+residue is plotted as the difference in Z-coordinate between Ca
+atoms. For an ideal helix this is 0.15 nm<br>
+<b>4.</b> Total helix length (file len-ahx.<a href="xvg.html">xvg</a>). The total length
+of the
+helix in nm. This is simply the average rise (see above) times the
+number of helical residues (see below).<br>
+<b>5.</b> Number of helical residues (file n-ahx.<a href="xvg.html">xvg</a>). The title says
+it all.<br>
+<b>6.</b> Helix Dipole, backbone only (file dip-ahx.<a href="xvg.html">xvg</a>).<br>
+<b>7.</b> RMS deviation from ideal helix, calculated for the Calpha
+atoms only (file rms-ahx.<a href="xvg.html">xvg</a>).<br>
+<b>8.</b> Average Calpha-Calpha dihedral angle (file phi-ahx.<a href="xvg.html">xvg</a>).<br>
+<b>9.</b> Average Phi and Psi angles (file phipsi.<a href="xvg.html">xvg</a>).<br>
+<b>10.</b> Ellipticity at 222 nm according to <it>Hirst and Brooks</it>
+<p>
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-to</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="g87.html"> gtraj.g87</a></tt> </TD><TD> Output, Opt. </TD><TD> Gromos-87 ASCII trajectory format </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-cz</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> zconf.gro</a></tt> </TD><TD> Output </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-co</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> waver.gro</a></tt> </TD><TD> Output </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-r0</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> The first residue number in the sequence </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]q</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Check at every step which part of the sequence is helical </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]F</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Toggle fit to a perfect helix </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]db</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print debug info </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]ev</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Write a new 'trajectory' file for ED </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ahxstart</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> First residue in helix </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ahxend</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Last residue in helix </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>g_lie</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>g_lie</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+g_lie computes a free energy estimate based on an energy analysis
+from. One needs an energy file with the following components:
+Coul (A-B) LJ-SR (A-B) etc.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> ener.edr</a></tt> </TD><TD> Input </TD><TD> Generic energy: <a href="edr.html">edr</a> <a href="ene.html">ene</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> lie.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-Elj</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Lennard-Jones interaction between ligand and solvent </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-Eqq</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Coulomb interaction between ligand and solvent </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-Clj</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.181</tt> </TD><TD> Factor in the LIE equation for Lennard-Jones component of energy </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-Cqq</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Factor in the LIE equation for Coulomb component of energy </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ligand</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Name of the ligand in the energy file </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>g_mdmat</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>g_mdmat</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+g_mdmat makes distance matrices consisting of the smallest distance
+between residue pairs. With -frames these distance matrices can be
+stored as a function
+of time, to be able to see differences in tertiary structure as a
+funcion of time. If you choose your options unwise, this may generate
+a large output file. Default only an averaged matrix over the whole
+trajectory is output.
+Also a count of the number of different atomic contacts between
+residues over the whole trajectory can be made.
+The output can be processed with <a href="xpm2ps.html">xpm2ps</a> to make a PostScript (tm) plot.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-mean</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html"> dm.xpm</a></tt> </TD><TD> Output </TD><TD> X PixMap compatible matrix file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-frames</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html"> dmf.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-no</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> num.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-t</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 1.5</tt> </TD><TD> trunc distance </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nlevels</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>40</tt> </TD><TD> Discretize distance in # levels </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>g_mindist</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>g_mindist</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+g_mindist computes the distance between one group and a number of
+other groups.
+Both the minimum distance and the number of contacts within a given
+distance are written to two separate output files.<p>
+With option <tt>-pi</tt> the minimum distance of a group to its
+periodic image is plotted. This is useful for checking if a protein
+has seen its periodic image during a simulation. Only one shift in
+each direction is considered, giving a total of 26 shifts.
+It also plots the maximum distance within the group and the lengths
+of the three box vectors.
+This option is very slow.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input, Opt. </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-od</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> mindist.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-on</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> numcont.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="out.html">atm-pair.out</a></tt> </TD><TD> Output </TD><TD> Generic output file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]matrix</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Calculate half a matrix of group-group distances </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-d</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.6</tt> </TD><TD> Distance for contacts </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]pi</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Calculate minimum distance with periodic images </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>g_morph</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>g_morph</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+g_morph does a linear interpolation of conformations in order to
+create intermediates. Of course these are completely unphysical, but
+that you may try to justify yourself. Output is in the form of a
+generic trajectory. The number of intermediates can be controlled with
+the -ninterm flag. The first and last flag correspond to the way of
+interpolating: 0 corresponds to input structure 1 while
+1 corresponds to input strucutre 2.
+If you specify first < 0 or last > 1 extrapolation will be
+on the path from input structure x1 to x2. In general the coordinates
+of the intermediate x(i) out of N total intermidates correspond to:<p>
+x(i) = x1 + (first+(i/(N-1))*(last-first))*(x2-x1)<p>
+Finally the RMSD with respect to both input structures can be computed
+if explicitly selected (-or option). In that case an index file may be
+read to select what group RMS is computed from.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f1</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> conf1.gro</a></tt> </TD><TD> Input </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f2</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> conf2.gro</a></tt> </TD><TD> Input </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> interm.xtc</a></tt> </TD><TD> Output </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-or</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">rms-interm.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ninterm</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>11</tt> </TD><TD> Number of intermediates </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-first</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Corresponds to first generated structure (0 is input x0, see above) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-last</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 1</tt> </TD><TD> Corresponds to last generated structure (1 is input x1, see above) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]fit</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Do a least squares fit of the second to the first structure before interpolating </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>g_msd</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>g_msd</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+g_msd computes the mean square displacement (MSD) of atoms from
+their initial positions. This provides an easy way to compute
+the diffusion constant using the Einstein relation.
+The diffusion constant is calculated by least squares fitting a
+straight line through the MSD from <tt>-beginfit</tt> to
+<tt>-endfit</tt>. An error estimate given, which is the difference
+of the diffusion coefficients obtained from fits over the two halfs
+of the fit interval.<p>
+Option <tt>-mol</tt> plots the MSD for molecules, this implies
+<tt>-mw</tt>, i.e. for each inidividual molecule an diffusion constant
+is computed. When using an index file, it should contain molecule
+numbers instead of atom numbers.
+Using this option one also gets an accurate error estimate
+based on the statistics between individual molecules. Since one usually
+is interested in self-diffusion at infinite dilution this is probably
+the most useful number.<p>
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> msd.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-mol</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">diff_mol.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: ps, fs, ns, us, ms, s, m or h </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-type</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>no</tt> </TD><TD> Compute diffusion coefficient in one direction: no, x, y or z </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-lateral</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>no</tt> </TD><TD> Calculate the lateral diffusion in a plane perpendicular to: no, x, y or z </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ngroup</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Number of groups to calculate MSD for </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]mw</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Mass weighted MSD </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-trestart</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Time between restarting points in trajectory (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-beginfit</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Start time for fitting the MSD (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-endfit</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> End time for fitting the MSD (ps), -1 is till end </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>g_nmeig</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>g_nmeig</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+g_nmeig calculates the eigenvectors/values of a (Hessian) matrix,
+which can be calculated with <tt><a href="nmrun.html">nmrun</a></tt>.
+The eigenvectors are written to a trajectory file (<tt>-v</tt>).
+The structure is written first with t=0. The eigenvectors
+are written as frames with the eigenvector number as timestamp.
+The eigenvectors can be analyzed with <tt><a href="g_anaeig.html">g_anaeig</a></tt>.
+An ensemble of structures can be generated from the eigenvectors with
+<tt><a href="g_nmens.html">g_nmens</a></tt>.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="mtx.html"> hessian.mtx</a></tt> </TD><TD> Input </TD><TD> Hessian matrix </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">eigenval.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-v</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">eigenvec.trr</a></tt> </TD><TD> Output </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]m</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Divide elements of Hessian by product of sqrt(mass) of involved atoms prior to diagonalization. This should be used for 'Normal Modes' analysis </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-first</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> First eigenvector to write away </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-last</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>100</tt> </TD><TD> Last eigenvector to write away </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>g_nmens</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>g_nmens</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+<tt>g_nmens</tt> generates an ensemble around an average structure
+in a subspace which is defined by a set of normal modes (eigenvectors).
+The eigenvectors are assumed to be mass-weighted.
+The position along each eigenvector is randomly taken from a Gaussian
+distribution with variance kT/eigenvalue.<p>
+By default the starting eigenvector is set to 7, since the first six
+normal modes are the translational and rotational degrees of freedom.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-v</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">eigenvec.trr</a></tt> </TD><TD> Input </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">eigenval.xvg</a></tt> </TD><TD> Input </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">ensemble.xtc</a></tt> </TD><TD> Output </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-temp</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 300</tt> </TD><TD> Temperature in Kelvin </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-seed</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Random seed, -1 generates a seed from time and pid </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-num</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>100</tt> </TD><TD> Number of structures to generate </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-first</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>7</tt> </TD><TD> First eigenvector to use (-1 is select) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-last</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Last eigenvector to use (-1 is till the last) </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>g_order</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>g_order</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+Compute the order parameter per atom for carbon tails. For atom i the
+vector i-1, i+1 is used together with an axis. The index file has to contain
+a group with all equivalent atoms in all tails for each atom the
+order parameter has to be calculated for. The program can also give all
+diagonal elements of the order tensor and even calculate the deuterium
+order parameter Scd (default). If the option -szonly is given, only one
+order tensor component (specified by the -d option) is given and the
+order parameter per slice is calculated as well. If -szonly is not
+selected, all diagonal elements and the deuterium order parameter is
+given.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> order.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-od</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> deuter.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-os</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> sliced.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-d</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>z</tt> </TD><TD> Direction of the normal on the membrane: z, x or y </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-sl</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Calculate order parameter as function of boxlength, dividing the box in #nr slices. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]szonly</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Only give Sz element of order tensor. (axis can be specified with -d) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]unsat</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Calculate order parameters for unsaturated carbons. Note that this cannot be mixed with normal order parameters. </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>g_potential</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>g_potential</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+Compute the electrostatical potential across the box. The potential iscalculated by first summing the charges per slice and then integratingtwice of this charge distribution. Periodic boundaries are not taken into account. Reference of potential is taken to be the left side ofthe box. It's also possible to calculate the potential in sphericalcoordinates as function of r by calculating a charge distribution inspherical slices and twice integrating them. epsilon_r is taken as 1,2 is more appropriate in many cases
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">potential.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-oc</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> charge.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-of</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> field.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-d</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>Z</tt> </TD><TD> Take the normal on the membrane in direction X, Y or Z. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-sl</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>10</tt> </TD><TD> Calculate potential as function of boxlength, dividing the box in #nr slices. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-cb</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Discard first #nr slices of box for integration </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ce</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Discard last #nr slices of box for integration </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-tz</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Translate all coordinates <distance> in the direction of the box </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]spherical</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Calculate spherical thingie </TD></TD>
+</TABLE>
+<P>
+<H3>Diagnostics</H3>
+<UL>
+<LI>Discarding slices for integration should not be necessary.
+</UL>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>g_rama</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>g_rama</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+g_rama selects the Phi/Psi dihedral combinations from your topology file
+and computes these as a function of time.
+Using simple Unix tools such as <it>grep</it> you can select out
+specific residues.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> rama.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>g_rdf</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>g_rdf</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+The structure of liquids can be studied by either neutron or X-ray
+scattering. The most common way to describe liquid structure is by a
+radial distribution function. However, this is not easy to obtain from
+a scattering experiment.<p>
+g_rdf calculates radial distribution functions in different ways.
+The normal method is around a (set of) particle(s), the other method
+is around the center of mass of a set of particles.<p>
+If a run input file is supplied (<tt>-s</tt>), exclusions defined
+in that file are taken into account when calculating the rdf.
+The option <tt>-cut</tt> is meant as an alternative way to avoid
+intramolecular peaks in the rdf plot.
+It is however better to supply a run input file with a higher number of
+exclusions. For eg. benzene a topology with nrexcl set to 5
+would eliminate all intramolecular contributions to the rdf.
+Note that all atoms in the selected groups are used, also the ones
+that don't have Lennard-Jones interactions.<p>
+Option <tt>-cn</tt> produces the cumulative number rdf.<p>To bridge the gap between theory and experiment structure factors can
+be computed (option <tt>-sq</tt>). The algorithm uses FFT, the gridspacing of which is determined by option <tt>-grid</tt>.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input, Opt. </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> rdf.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-sq</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> sq.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-cn</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> rdf_cn.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-hq</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> hq.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-image</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html"> sq.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-bin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.001</tt> </TD><TD> Binwidth (nm) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]com</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> RDF with respect to the center of mass of first group </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-cut</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Shortest distance (nm) to be considered </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-fade</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> From this distance onwards the RDF is tranformed by g'(r) = 1 + [g(r)-1] exp(-(r/fade-1)^2 to make it go to 1 smoothly. If fade is 0.0 nothing is done. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-grid</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.05</tt> </TD><TD> Grid spacing (in nm) for FFTs when computing structure factors </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nlevel</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>20</tt> </TD><TD> Number of different colors in the diffraction image </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-wave</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.1</tt> </TD><TD> Wavelength for X-rays/Neutrons for scattering. 0.1 nm corresponds to roughly 12 keV </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>g_rms</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>g_rms</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+g_rms compares two structures by computing the root mean square
+deviation (RMSD), the size-independent 'rho' similarity parameter
+(rho) or the scaled rho (rhosc),
+reference Maiorov & Crippen, PROTEINS 22, 273 (1995).
+This is selected by <tt>-what</tt>.<p>Each structure from a trajectory (<tt>-f</tt>) is compared to a
+reference structure from a run input file by least-squares fitting
+the structures on <a href="top.html">top</a> of each other. The reference structure is taken
+from the structure file (<tt>-s</tt>).<p>
+With option <tt>-mir</tt> also a comparison with the mirror image of
+the reference structure is calculated.<p>
+Option <tt>-prev</tt> produces the comparison with a previous frame.<p>
+Option <tt>-m</tt> produces a matrix in <tt>.<a href="xpm.html">xpm</a></tt> format of
+comparison values of each structure in the trajectory with respect to
+each other structure. This file can be visualized with for instance
+<tt>xv</tt> and can be converted to postscript with <tt><a href="xpm2ps.html">xpm2ps</a></tt>.<p>
+All the structures are fitted pairwise.<p>
+With <tt>-f2</tt>, the 'other structures' are taken from a second
+trajectory.<p>
+Option <tt>-bin</tt> does a binary dump of the comparison matrix.<p>
+Option <tt>-bm</tt> produces a matrix of average bond angle deviations
+analogously to the <tt>-m</tt> option. Only bonds between atoms in the
+comparison group are considered.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f2</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> rmsd.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-mir</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> rmsdmir.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-a</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> avgrp.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-dist</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">rmsd-dist.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-m</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html"> rmsd.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-bin</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="dat.html"> rmsd.dat</a></tt> </TD><TD> Output, Opt. </TD><TD> Generic data file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-bm</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html"> bond.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: ps, fs, ns, us, ms, s, m or h </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-what</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>rmsd</tt> </TD><TD> Structural difference measure: rmsd, rho or rhosc </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> PBC check </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]fit</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Fit to reference structure </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-prev</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Compare with previous frame </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]split</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Split graph where time is zero </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-skip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Only write every nr-th frame to matrix </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-skip2</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Only write every nr-th frame to matrix </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-max</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Maximum level in comparison matrix </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-min</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Minimum level in comparison matrix </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-bmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Maximum level in bond angle matrix </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-bmin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Minimum level in bond angle matrix </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nlevels</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>80</tt> </TD><TD> Number of levels in the matrices </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>g_rmsdist</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>g_rmsdist</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+g_rmsdist computes the root mean square deviation of atom distances,
+which has the advantage that no fit is needed like in standard RMS
+deviation as computed by <a href="g_rms.html">g_rms</a>.
+The reference structure is taken from the structure file.
+The rmsd at time t is calculated as the rms
+of the differences in distance between atom-pairs in the reference
+structure and the structure at time t.<p>
+g_rmsdist can also produce matrices of the rms distances, rms distances
+scaled with the mean distance and the mean distances and matrices with
+NMR averaged distances (1/r^3 and 1/r^6 averaging). Finally, lists
+of atom pairs with 1/r^3 and 1/r^6 averaged distance below the
+maximum distance (<tt>-max</tt>, which will default to 0.6 in this case)
+can be generated, by default averaging over equivalent hydrogens
+(all triplets of hydrogens named *[123]). Additionally a list of
+equivalent atoms can be supplied (<tt>-equiv</tt>), each line containing
+a set of equivalent atoms specified as residue number and name and
+atom name; e.g.:<p>
+<tt>3 SER HB1 3 SER HB2</tt><p>
+Residue and atom names must exactly match those in the structure
+file, including case. Specifying non-sequential atoms is undefined.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-equiv</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="dat.html"> equiv.dat</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic data file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">distrmsd.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-rms</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html"> rmsdist.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-scl</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html">rmsscale.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-mean</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html"> rmsmean.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-nmr3</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html"> nmr3.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-nmr6</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html"> nmr6.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-noe</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="dat.html"> noe.dat</a></tt> </TD><TD> Output, Opt. </TD><TD> Generic data file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nlevels</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>40</tt> </TD><TD> Discretize rms in # levels </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-max</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Maximum level in matrices </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]sumh</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> average distance over equivalent hydrogens </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>g_rmsf</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>g_rmsf</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard
+deviation) of atomic positions
+after first fitting to a reference frame.<p>
+With option <tt>-oq</tt> the RMSF values are converted to B-factor
+values, which are written to a <a href="pdb.html">pdb</a> file with the coordinates, of the
+structure file, or of a <a href="pdb.html">pdb</a> file when <tt>-q</tt> is specified.
+Option <tt>-ox</tt> writes the B-factors to a file with the average
+coordinates.<p>
+With the option <tt>-od</tt> the root mean square deviation with
+respect to the reference structure is calculated.<p>
+With the option <tt>aniso</tt> g_rmsf will compute anisotropic
+temperature factors and then it will also output average coordinates
+and a <a href="pdb.html">pdb</a> file with ANISOU records (corresonding to the <tt>-oq</tt>
+or <tt>-ox</tt> option). Please note that the U values
+are orientation dependent, so before comparison with experimental data
+you should verify that you fit to the experimental coordinates.<p>
+When a <a href="pdb.html">pdb</a> input file is passed to the program and the <tt>-aniso</tt>
+flag is set
+a correlation plot of the Uij will be created, if any anisotropic
+temperature factors are present in the <a href="pdb.html">pdb</a> file.<p>
+With option <tt>-dir</tt> the average MSF (3x3) matrix is diagonalized.
+This shows the directions in which the atoms fluctuate the most and
+the least.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-q</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="pdb.html"> eiwit.pdb</a></tt> </TD><TD> Input, Opt. </TD><TD> Protein data bank file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-oq</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="pdb.html"> bfac.pdb</a></tt> </TD><TD> Output, Opt. </TD><TD> Protein data bank file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-ox</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="pdb.html"> xaver.pdb</a></tt> </TD><TD> Output, Opt. </TD><TD> Protein data bank file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> rmsf.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-od</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> rmsdev.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-oc</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> correl.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-dir</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html"> rmsf.log</a></tt> </TD><TD> Output, Opt. </TD><TD> Log file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]res</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Calculate averages for each residue </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]aniso</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Compute anisotropic termperature factors </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>g_rotacf</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>g_rotacf</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+g_rotacf calculates the rotational correlation function
+for molecules. Three atoms (i,j,k) must be given in the index
+file, defining two vectors ij and jk. The rotational acf
+is calculated as the autocorrelation function of the vector
+n = ij x jk, i.e. the cross product of the two vectors.
+Since three atoms span a plane, the order of the three atoms
+does not matter. Optionally, controlled by the -d switch, you can
+calculate the rotational correlation function for linear molecules
+by specifying two atoms (i,j) in the index file.
+<p>
+EXAMPLES<p>
+g_rotacf -P 1 -nparm 2 -fft -n index -o rotacf-x-P1
+-fa expfit-x-P1 -beginfit 2.5 -endfit 20.0<p>
+This will calculate the rotational correlation function using a first
+order Legendre polynomial of the angle of a vector defined by the index
+file. The correlation function will be fitted from 2.5 ps till 20.0 ps
+to a two parameter exponential
+
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> rotacf.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]d</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use index doublets (vectors) for correlation function instead of triplets (planes) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]aver</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Average over molecules </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-acflen</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Length of the ACF, default is half the number of frames </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Normalize ACF </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-P</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or 3 </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: none, exp, aexp, exp_exp or vac </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ncskip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip N points in the output file of correlation functions </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-beginfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Time where to begin the exponential fit of the correlation function </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-endfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Time where to end the exponential fit of the correlation function, -1 is till the end </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>g_saltbr</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>g_saltbr</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+g_saltbr plots the difference between all combination of charged groups
+as a function of time. The groups are combined in different ways.A minimum distance can be given, (eg. the cut-off), then groups
+that are never closer than that distance will not be plotted.<br>
+Output will be in a number of fixed filenames, min-min.<a href="xvg.html">xvg</a>,min-plus.<a href="xvg.html">xvg</a>
+and plus-plus.<a href="xvg.html">xvg</a>, or files for every individual ion-pair if selected
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-t</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 1000</tt> </TD><TD> trunc distance </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]sep</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use separate files for each interaction (may be MANY) </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>g_sas</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>g_sas</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+g_sas computes hydrophobic and total solvent accessible surface area.
+As a side effect the Connolly surface can be generated as well in
+a <a href="pdb.html">pdb</a> file where the nodes are represented as atoms and the vertices
+connecting the nearest nodes as CONECT records. The area can be plotted
+per atom and per residue as well (option -ao). In combination with
+the latter option an <tt><a href="itp.html">itp</a></tt> file can be generated (option -i)
+which can be used to restrain surface atoms.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> area.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-r</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> resarea.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-q</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="pdb.html">connelly.pdb</a></tt> </TD><TD> Output, Opt. </TD><TD> Protein data bank file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-ao</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">atomarea.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-i</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="itp.html"> surfat.itp</a></tt> </TD><TD> Output, Opt. </TD><TD> Include file for topology </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-solsize</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.14</tt> </TD><TD> Radius of the solvent probe (nm) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ndots</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>24</tt> </TD><TD> Number of dots per sphere, more dots means more accuracy </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-qmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.2</tt> </TD><TD> The maximum charge (e, absolute value) of a hydrophobic atom </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-minarea</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.5</tt> </TD><TD> The maximum charge (e, absolute value) of a hydrophobic atom </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-skip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Do only every nth frame </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]prot</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Output the protein to the connelly <a href="pdb.html">pdb</a> file too </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>g_sgangle</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>g_sgangle</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+Compute the angle and distance between two groups.
+The groups are defined by a number of atoms given in an index file and
+may be two or three atoms in size.
+The angles calculated depend on the order in which the atoms are
+given. Giving for instance 5 6 will rotate the vector 5-6 with
+180 degrees compared to giving 6 5. <p>If three atoms are given,
+the normal on the plane spanned by those three atoms will be
+calculated, using the formula P1P2 x P1P3.
+The cos of the angle is calculated, using the inproduct of the two
+normalized vectors.<p>
+Here is what some of the file options do:<br>
+-oa: Angle between the two groups specified in the index file. If a group contains three atoms the normal to the plane defined by those three atoms will be used. If a group contains two atoms, the vector defined by those two atoms will be used.<br>
+-od: Distance between two groups. Distance is taken from the center of one group to the center of the other group.<br>
+-od1: If one plane and one vector is given, the distances for each of the atoms from the center of the plane is given seperately.<br>
+-od2: For two planes this option has no meaning.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-oa</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">sg_angle.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-od</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> sg_dist.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-od1</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">sg_dist1.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-od2</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">sg_dist2.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>g_sorient</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>g_sorient</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+g_sorient analyzes solvent orientation around solutes.
+It calculates two angles between the vector from one or more
+reference positions to the first atom of each solvent molecule:<br>theta1: the angle with the vector from the first atom of the solvent
+molecule to the midpoint between atoms 2 and 3.<br>
+theta2: the angle with the normal of the solvent plane, defined by the
+same three atoms.<br>
+The reference can be a set of atoms or
+the center of mass of a set of atoms. The group of solvent atoms should
+consist of 3 atoms per solvent molecule.
+Only solvent molecules between <tt>-rmin</tt> and <tt>-rmax</tt> are
+considered each frame.<p>
+<tt>-o</tt>: angle distribution of theta1.<p>
+<tt>-no</tt>: angle distribution of theta2.<p>
+<tt>-ro</tt>: <cos(theta1)> and <3cos^2(theta2)-1> as a function of the
+distance.<p>
+<tt>-ro</tt>: the sum over all solvent molecules within distance r
+of cos(theta1) and 3cos^2(theta2)-1 as a function of r.<p>
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> sori.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-no</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> snor.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-ro</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> sord.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-co</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> scum.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]com</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use the center of mass as the reference postion </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-rmin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Minimum distance </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-rmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.5</tt> </TD><TD> Maximum distance </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nbin</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>20</tt> </TD><TD> Number of bins </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>g_tcaf</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>g_tcaf</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+g_tcaf computes tranverse current autocorrelations.
+These are used to estimate the shear viscosity eta.
+For details see: Palmer, JCP 49 (1994) pp 359-366.<p>
+Transverse currents are calculated using the
+k-vectors (1,0,0) and (2,0,0) each also in the y- and z-direction,
+(1,1,0) and (1,-1,0) each also in the 2 other plains (these vectors
+are not independent) and (1,1,1) and the 3 other box diagonals (also
+not independent). For each k-vector the sine and cosine are used, in
+combination with the velocity in 2 perpendicular directions. This gives
+a total of 16*2*2=64 transverse currents. One autocorrelation is
+calculated fitted for each k-vector, which gives 16 tcaf's. Each of
+these tcaf's is fitted to f(t) = exp(-v)(cosh(Wv) + 1/W sinh(Wv)),
+v = -t/(2 tau), W = sqrt(1 - 4 tau eta/rho k^2), which gives 16 tau's
+and eta's. The fit weights decay with time as exp(-t/wt), the tcaf and
+fit are calculated up to time 5*wt.
+The eta's should be fitted to 1 - a eta(k) k^2, from which
+one can estimate the shear viscosity at k=0.<p>
+When the box is cubic, one can use the option <tt>-oc</tt>, which
+averages the tcaf's over all k-vectors with the same length.
+This results in more accurate tcaf's.
+Both the cubic tcaf's and fits are written to <tt>-oc</tt>
+The cubic eta estimates are also written to <tt>-ov</tt>.<p>
+With option <tt>-mol</tt> the transverse current is determined of
+molecules instead of atoms. In this case the index group should
+consist of molecule numbers instead of atom numbers.<p>
+The k-dependent viscosities in the <tt>-ov</tt> file should be
+fitted to eta(k) = eta0 (1 - a k^2) to obtain the viscosity at
+infinite wavelength.<p>
+NOTE: make sure you write coordinates and velocities often enough.
+The initial, non-exponential, part of the autocorrelation function
+is very important for obtaining a good fit.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.trr</a></tt> </TD><TD> Input </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input, Opt. </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-ot</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">transcur.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-oa</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">tcaf_all.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> tcaf.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-of</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">tcaf_fit.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-oc</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">tcaf_cub.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-ov</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> visc_k.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]mol</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Calculate tcaf of molecules </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]k34</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Also use k=(3,0,0) and k=(4,0,0) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-wt</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 5</tt> </TD><TD> Exponential decay time for the TCAF fit weights </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>g_traj</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>g_traj</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+g_traj plots coordinates, velocities, forces and/or the box.
+With <tt>-com</tt> the coordinates, velocities and forces are
+calculated for the center of mass of each group.
+When <tt>-mol</tt> is set, the numbers in the index file are
+interpreted as molecule numbers and the same procedure as with
+<tt>-com</tt> is used for each molecule.<p>
+Option <tt>-ot</tt> plots the temperature of each group.
+This implies <tt>-com</tt>.<p>
+Option <tt>-ekr</tt> plots the rotational kinetic energy of each group.
+This implies <tt>-com</tt>.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-ox</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> coord.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-ov</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> veloc.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-of</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> force.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-ob</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> box.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-ot</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> temp.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-ekr</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> ekrot.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]com</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Plot data for the com of each group </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]mol</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Index contains molecule numbers iso atom numbers </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]nojump</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Remove jumps of atoms across the box </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]x</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Plot X-component </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]y</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Plot Y-component </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]z</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Plot Z-component </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]len</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Plot vector length </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>g_velacc</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>g_velacc</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+g_velacc computes the velocity autocorrelation function.
+When the <tt>-s</tt> option is used, the momentum autocorrelation
+function is calculated.<p>
+With option <tt>-mol</tt> the momentum autocorrelation function of
+molecules is calculated. In this case the index group should consist
+of molecule numbers instead of atom numbers.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.trr</a></tt> </TD><TD> Input </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input, Opt. </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> vac.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]mol</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Calculate vac of molecules </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-acflen</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Length of the ACF, default is half the number of frames </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Normalize ACF </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-P</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or 3 </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: none, exp, aexp, exp_exp or vac </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ncskip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip N points in the output file of correlation functions </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-beginfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Time where to begin the exponential fit of the correlation function </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-endfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Time where to end the exponential fit of the correlation function, -1 is till the end </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>genbox</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>genbox</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+Genbox can do one of 3 things:<p>
+1) Generate a box of solvent. Specify -cs and -box. Or specify -cs and
+-cp with a structure file with a box, but without atoms.<p>
+2) Solvate a solute configuration, eg. a protein, in a bath of solvent
+molecules. Specify <tt>-cp</tt> (solute) and <tt>-cs</tt> (solvent).
+The box specified in the solute coordinate file (<tt>-cp</tt>) is used,
+unless <tt>-box</tt> is set, which also centers the solute.
+The program <tt><a href="editconf.html">editconf</a></tt> has more sophisticated options to change
+the box and center the solute.
+Solvent molecules are removed from the box where the
+distance between any atom of the solute molecule(s) and any atom of
+the solvent molecule is less than the sum of the VanderWaals radii of
+both atoms. A database (<tt>vdwradii.<a href="dat.html">dat</a></tt>) of VanderWaals radii is
+read by the program, atoms not in the database are
+assigned a default distance <tt>-vdw</tt>.<p>
+3) Insert a number (<tt>-nmol</tt>) of extra molecules (<tt>-ci</tt>)
+at random positions.
+The program iterates until <tt>nmol</tt> molecules
+have been inserted in the box. To test whether an insertion is
+successful the same VanderWaals criterium is used as for removal of
+solvent molecules. When no appropriately
+sized holes (holes that can hold an extra molecule) are available the
+program tries for <tt>-nmol</tt> * <tt>-try</tt> times before giving up.
+Increase -try if you have several small holes to fill.<p>
+The default solvent is Simple Point Charge water (SPC). The coordinates
+for this are read from <tt>$GMXLIB/spc216.<a href="gro.html">gro</a></tt>. Other
+solvents are also supported, as well as mixed solvents. The
+only restriction to solvent types is that a solvent molecule consists
+of exactly one residue. The residue information in the coordinate
+files is used, and should therefore be more or less consistent.
+In practice this means that two subsequent solvent molecules in the
+solvent coordinate file should have different residue number.
+The box of solute is built by stacking the coordinates read from
+the coordinate file. This means that these coordinates should be
+equlibrated in periodic boundary conditions to ensure a good
+alignment of molecules on the stacking interfaces.<p>
+The program can optionally rotate the solute molecule to align the
+longest molecule axis along a box edge. This way the amount of solvent
+molecules necessary is reduced.
+It should be kept in mind that this only works for
+short simulations, as eg. an alpha-helical peptide in solution can
+rotate over 90 degrees, within 500 ps. In general it is therefore
+better to make a more or less cubic box.<p>
+Setting -shell larger than zero will place a layer of water of
+the specified thickness (nm) around the solute. Hint: it is a good
+idea to put the protein in the center of a box first (using <a href="editconf.html">editconf</a>).
+<p>
+Finally, genbox will optionally remove lines from your topology file in
+which a number of solvent molecules is already added, and adds a
+line with the total number of solvent molecules in your coordinate file.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-cp</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> protein.gro</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-cs</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> spc216.gro</a></tt> </TD><TD> Input, Opt., Lib. </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-ci</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> insert.gro</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> out.gro</a></tt> </TD><TD> Output </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-p</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="top.html"> topol.top</a></tt> </TD><TD> In/Out, Opt. </TD><TD> Topology file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-box</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 0</tt> </TD><TD> box size </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nmol</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> no of extra molecules to insert </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-try</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>10</tt> </TD><TD> try inserting -nmol*-try times </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-seed</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1997</tt> </TD><TD> random generator seed </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-vdwd</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.105</tt> </TD><TD> default vdwaals distance </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-shell</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> thickness of optional water layer around solute </TD></TD>
+</TABLE>
+<P>
+<H3>Diagnostics</H3>
+<UL>
+<LI>Molecules must be whole in the initial configurations.
+<LI>At the moment -ci only works when inserting one molecule.
+</UL>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>genconf</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>genconf</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+genconf multiplies a given coordinate file by simply stacking them
+on <a href="top.html">top</a> of each other, like a small child playing with wooden blocks.
+The program makes a grid of <it>user defined</it>
+proportions (<tt>-nbox</tt>),
+and interspaces the grid point with an extra space <tt>-dist</tt>.<p>
+When option <tt>-rot</tt> is used the program does not check for overlap
+between molecules on grid points. It is recommended to make the box in
+the input file at least as big as the coordinates +
+Van der Waals radius.<p>
+If the optional trajectory file is given, conformations are not
+generated, but read from this file and translated appropriately to
+build the grid.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> conf.gro</a></tt> </TD><TD> Input </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> out.gro</a></tt> </TD><TD> Output </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-trj</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nbox</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>1 1 1</tt> </TD><TD> Number of boxes </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dist</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 0</tt> </TD><TD> Distance between boxes </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-seed</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Random generator seed, if 0 generated from the time </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]rot</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Randomly rotate conformations </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]shuffle</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Random shuffling of molecules </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]sort</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Sort molecules on X coord </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-block</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Divide the box in blocks on this number of cpus </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nmolat</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>3</tt> </TD><TD> Number of atoms per molecule, assumed to start from 0. If you set this wrong, it will screw up your system! </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-maxrot</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>90 90 90</tt> </TD><TD> Maximum random rotation </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]renumber</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Renumber residues </TD></TD>
+</TABLE>
+<P>
+<H3>Diagnostics</H3>
+<UL>
+<LI>The program should allow for random displacement off lattice points.
+</UL>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>genion</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>genion</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+genion replaces solvent molecules by monoatomic ions at
+the position of the first atoms with the most favorable electrostatic
+potential or at random. The potential is calculated on all atoms, using
+normal GROMACS particle based methods (in contrast to other methods
+based on solving the Poisson-Boltzmann equation).
+The potential is recalculated after every ion insertion.
+If specified in the run input file, a reaction field or shift function
+can be used.
+The group of solvent molecules should be continuous and all molecules
+should have the same number of atoms.
+The user should add the ion molecules to the topology file and include
+the file <tt>ions.<a href="itp.html">itp</a></tt>.
+Ion names for Gromos96 should include the charge.<p>
+The potential can be written as B-factors
+in a <a href="pdb.html">pdb</a> file (for visualisation using e.g. rasmol).
+The unit of the potential is 0.001 kJ/(mol e).<p>
+For larger ions, e.g. sulfate we recommended to use <a href="genbox.html">genbox</a>.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> out.gro</a></tt> </TD><TD> Output </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-g</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html"> genion.log</a></tt> </TD><TD> Output </TD><TD> Log file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-pot</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="pdb.html"> pot.pdb</a></tt> </TD><TD> Output, Opt. </TD><TD> Protein data bank file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-np</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of positive ions </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-pname</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>Na</tt> </TD><TD> Name of the positive ion </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-pq</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 1</tt> </TD><TD> Charge of the positive ion </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nn</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of negative ions </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nname</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>Cl</tt> </TD><TD> Name of the negative ion </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nq</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Charge of the negative ion </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-rmin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.6</tt> </TD><TD> Minimum distance between ions </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]random</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use random placement of ions instead of based on potential. The rmin option should still work </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-seed</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1993</tt> </TD><TD> Seed for random number generator </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>genpr</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>genpr</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+genpr produces an include file for a topology containing
+a list of atom numbers and three force constants for the
+X, Y and Z direction. A single isotropic force constant may
+be given on the command line instead of three components.<p>
+WARNING: genpr only works for the first molecule.
+Position restraints are interactions within molecules, therefore
+they should be included within the correct <tt>[ moleculetype ]</tt>
+block in the topology. Since the atom numbers in every moleculetype
+in the topology start at 1 and the numbers in the input file for
+genpr number consecutively from 1, genpr will only produce a useful
+file for the first molecule.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> conf.gro</a></tt> </TD><TD> Input </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="itp.html"> posre.itp</a></tt> </TD><TD> Output </TD><TD> Include file for topology </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-fc</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>1000 1000 1000</tt> </TD><TD> force constants (kJ mol-1 nm-2) </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
<TITLE>Getting Started</TITLE>
<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso_8859_1">
</HEAD>
-<BODY >
-<h2>Contents</h2>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<h2>Getting Started</h2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Contents</H3>
+
<ul>
-<li><a href="#start">Getting started</a>
+<li><a href="#start">Introduction</a>
<ul>
<li><a href="#setup">Setting up your environment</a>
<li><a href="#examples">Examples</a>
</ul>
-<li><a href="#demo">GMX demo</a>
+<li><a href="#demo">The GROMACS demo</a>
<ul>
<li><a href="#top">Molecular topology file</a>
<li><a href="#gro">Molecular structure file</a>
<br><hr><br>
-<a name="start"><H1>Getting started.</A></H1>
+<a name="start"><H2>Introduction</A></H2>
In this chapter we assume the reader is familiar with Molecular
Dynamics and familiar with Unix, including the use of a text editor
such as <tt>emacs</tt> or <tt>vi</tt>. We furthermore assume the
software is installed properly on your system. When you see a line
-like
+like<p>
<PRE>
% ls -l
</PRE>
<TT>%</TT>) on your computer.
<P>We will also assume that you know where your version of GROMACS is
-installed. For local users in the Groningen MD group that is simply
-'~gmx', e.g. the GMXRC is located in ~gmx/GMXRC. For other users that
+installed. The default location is '/usr/local/gromacs', but for
+local users in the Groningen MD group it is simply
+'~gmx'. In the default case, the binaries are located in
+'/usr/local/gromacs/bin/<arch>', where <arch>
+is the architecture of your computer. For other users that
is probably not the case, contact your local system administrator for
-more information. The directories named in this section are valid for the
-Groningen MD group.
+more information..
-<P><H2><A NAME="setup">Setting up your environment</A></H2>
+<P><H3><A NAME="setup">Setting up your environment</A></H3>
-Edit your <TT>.cshrc</TT> file to include the following statement:
-<PRE>
-source ~gmx/GMXRC
-</PRE>
-which has some (system dependent) PATH settings etcetera. Then type
+The first step is to make sure the GROMACS binaries are in your path.
+On some systems they will simply be linked to /usr/local/bin and found
+automatically. If this is not the case on your machine you will have
+to edit the login file for your shell. If you use the C shell, this
+file is called <TT>.cshrc</TT> or <TT>.tcshrc</TT>, and located in
+your home directory. Add a line like:
<PRE>
-% source ~gmx/GMXRC
+setenv PATH "/usr/local/gromacs/bin/<arch>:${PATH}".
</PRE>
-to start right away, or, alternatively
-log off and on again to automatically source the environment.
+Issue this command at the prompt too, or
+log off and on again to automatically get the environment.
<P>
-Check if you now have the proper environment by
-<PRE>
-% echo $GMXHOME
-</PRE>
-It should read something like:
-<PRE>
-/home/gmx/gmx2.0
-</PRE>
-This is the directory in which the binaries and
-library files live. If you see nothing (a blank line) something is
-wrong with the installation, check with your system manager, or (if
-<EM>you</EM> are the system manager) you did something wrong
-somewhere <b>:(</b>
-<P><H2><A NAME="examples">Examples.</A></H2>
+<P><H3><A NAME="examples">Examples</A></H3>
Before starting the examples, you have to copy all the neccesary
files, to your own directory. Chdir to the directory you want to put
the examples directory. This directory (named <tt>tutor</tt>)
</PRE>
then copy the examples:
<PRE>
-% cp -r ~gmx/home2.0/tutor .
+% cp -r /usr/local/gromacs/share/tutor .
</PRE>
(NOTE: include the ``<TT>.</TT>'') You now have a subdirectory
<tt>tutor</tt>. Move there
<br><hr><br>
-<P><H1><A NAME="demo">GMX demo.</A></H1>
+<P><H2><A NAME="demo">The GROMACS demo</A></H2>
The demo is designed to demonstrate the user-friendlyness
-of the GROMACS software package. Start the demo by going
+of the GROMACS software package. The only non-friendly part is
+that it requires the C shell to run the script. If your shell
+is e.g. bash (common on Linux), first start the C shell with the
+command 'tcsh'. To run the demo, first move
to your <tt>tutor/gmxdemo</tt> directory:
<PRE>
% cd tutor/gmxdemo
-</PRE> Start the demo:
+</PRE> And then start the demo script:
<PRE>
% demo
</PRE>
<DL>
<DT>
-<B><A NAME="top">Molecular Topology file (<TT><a href="top.html">.top</a></TT>)</A></B>
+<h3><A NAME="top">Molecular Topology file (<TT><a href="top.html">.top</a></TT>)</A></h3>
<DD>
The molecular topology file is generated by the program <TT>
<a href="pdb2gmx.html">pdb2gmx</a></TT>. <a href="pdb2gmx.html">pdb2gmx</a> translates a <a href="pdb.html">pdb</a> structure file of any peptide
<P></P>
<DT>
-<B><A NAME="gro">Molecular Structure file (<TT><a href="gro.html">.gro</a></TT>, <TT><a href="pdb.html">.pdb</a></TT>)</A></B>
+<h3><A NAME="gro">Molecular Structure file (<TT><a href="gro.html">.gro</a></TT>, <TT><a href="pdb.html">.pdb</a></TT>)</A></h3>
<DD>
When the <a href="pdb2gmx.html">pdb2gmx</a> program is executed to generate a molecular
topology, it also translates the structure file (<TT><a href="pdb.html">.pdb</a></TT> file)
<P></P>
<DT>
-<B><A NAME="mdp">Molecular Dynamics parameter file (<TT><a href="mdp_opt.html">.mdp</a></TT>)</A></B>
+<h3><A NAME="mdp">Molecular Dynamics parameter file (<TT><a href="mdp_opt.html">.mdp</a></TT>)</A></h3>
<DD>
The Molecular Dynamics Parameter (<TT><a href="mdp_opt.html">.mdp</a></TT>) file contains all
information about the Molecular Dynamics simulation itself
<P></P>
<DT>
-<B><A NAME="ndx">Index file (<TT><a href="ndx.html">.ndx</a></TT>)</A></B>
+<h3><A NAME="ndx">Index file (<TT><a href="ndx.html">.ndx</a></TT>)</A></h3>
<DD>
Sometimes you may need an index file to specify actions on groups of atoms
(e.g. Temperature coupling, accelerations, freezing). Usually the default ibdex
<P></P>
<DT>
-<B><A NAME="tpr">Run input file (<TT><a href="tpr.html">.tpr</a></TT>)</A></B>
+<h3><A NAME="tpr">Run input file (<TT><a href="tpr.html">.tpr</a></TT>)</A></h3>
<DD>
The next step is to combine the molecular structure (<TT><a href="gro.html">.gro</a></TT> file),
topology (<TT><a href="top.html">.top</a></TT> file) MD-parameters (<TT><a href="mdp_opt.html">.mdp</a></TT> file) and
<P></P>
<DT>
-<B><A NAME="trx">Trajectory file (<TT><a href="trr.html">.trr</a></TT></A>)</B>
+<h3><A NAME="trx">Trajectory file (<TT><a href="trr.html">.trr</a></TT></A>)</h3>
<DD>
Once the run input file is available, we can start the
simulation. The program which starts the simulation is called
<br><hr><br>
-<P><H1><A NAME="water">Water</A></H1>
+<P><H2><A NAME="water">Water</A></H2>
Now you are going to simulate 216 molecules of SPC water
(<A HREF=#berendsen81>Berendsen <it>et al.</it>, 1981</A>)
in a rectangular box. In this example the GROMACS
<PRE>
% <a href="g_rdf.html">g_rdf</a> -f <a href="trr.html">water.trr</a> -n <a href="ndx.html">oxygen.ndx</a> -o <a href="xvg.html">rdf.xvg</a> -s <a href="tpr.html">water.tpr</a>
</PRE>
-view the output graph of <TT><a href="g_rdf.html">g_rdf</a></TT>
+view the output graph of <TT><a href="g_rdf.html">g_rdf</a></TT>.
+The file is already prepared to produce a nice graph in Grace
+(formerly Xmgr). Just type (<TT>xmgr</TT> works fine too)
<PRE>
-% x
vgr <a href="xvg.html">rdf.xvg</a>
+% x
mgrace <a href="xvg.html">rdf.xvg</a>
</PRE>
Which shows you the radial distribution function for Oxygen-Oxygen in
SPC water. </p>
<br><hr><br>
-<P><H1><A NAME="spep">Ribonuclease S-peptide.</A></H1>
-Ribonuclease A is a digestive enzyme, secreted by the pancreas. The enzyme
+<A NAME="spep"><H2>Ribonuclease S-peptide</A></H2>
+
+<p>Ribonuclease A is a digestive enzyme, secreted by the pancreas. The enzyme
can be cleaved by subtilisin at a single peptide bond to yield
Ribonuclease-S, a catalytically active complex of an S-peptide moiety
(residues 1-20) and an S-protein moiety (residues 21-124), bound together
Have a look at the file
<PRE>
% more <a href="pdb.html">speptide.pdb</a>
-</PRE>
+</PRE><p>
If you have access to a molecular
graphics program such as rasmol, xmol,
or a commercial package,
you can look at the molecule on screen, eg:
<PRE>
% rasmol <a href="pdb.html">speptide.pdb</a>
-</PRE>
+</PRE><p>
The following steps have to be taken to perform a simulation of the peptide.
<ol>
<li> Perform a short MD run with position restraints on the peptide
<li> Perform full MD without restraints
<li> Analysis
-</ol>
+</ol><p>
We will describe in detail how such a simulation can be done,
starting from a pdb-file.
format. This can be done with the <a href="pdb2gmx.html">pdb2gmx</a> program:
<PRE>
% <a href="pdb2gmx.html">pdb2gmx</a> -f <a href="pdb.html">speptide.pdb</a> -p <a href="top.html">speptide.top</a> -o <a href="gro.html">speptide.gro</a>
-</PRE>
+</PRE><p>
Note that the correct file extension are added automatically to the
filenames on the command line.
You will only be asked to choose a forcefield, choose 0, but you can also
You can type
<PRE>
% <a href="pdb2gmx.html">pdb2gmx</a> -h
-</PRE>
+</PRE><p>
to see the available options.
<P>
The <a href="pdb2gmx.html">
Now have a look at the output from <a href="pdb2gmx.html">pdb2gmx</a>,
<PRE>
% more <a href="gro.html">speptide.gro</a>
-</PRE>
+</PRE><p>
You will see a close resemblance to the <a href="pdb.html">pdb</a> file, only the layout of
the file is a bit different.
Also do have a look at the topology
<PRE>
% more <a href="top.html">speptide.top</a>
-</PRE>
+</PRE><p>
You will see a large file containing the atom types, the physical
bonds between atoms, etcetera.
<P><H3><A NAME="solvate">
-Solvate the peptide in a periodic box filled with water</A></H3>
+Solvate the peptide in a periodic box filled with water</A></H3><p>
This is done using the programs
<a href="editconf.html">editconf</a> and
<a href="genbox.html">genbox</a>.
<PRE>
% <a href="editconf.html">editconf</a> -f speptide -o -dc 0.5<BR>
% <a href="genbox.html">genbox</a> -cp out -cs -p speptide -o b4em
-</PRE>
+</PRE><p>
The program prints some lines of user information, like the volume of
the box and the number of water molecules added to your
peptide. <TT><a href="genbox.html">genbox</a></TT>
<TT><a href="top.html">speptide.top</a></TT> file
<PRE>
% tail <a href="top.html">speptide.top</a>
-</PRE>
+</PRE><p>
You will see some lines like
<PRE>
[ system ]
; Name Number
Protein 1
SOL N
-</PRE>
+</PRE><p>
where <tt>N</tt> is the number of water molecules added to your system by
<TT><a href="genbox.html">genbox</a></TT>.
<P>
<A HREF=#mierke91>Mierke & Kessler, 1991</A>.
<P><H3><A NAME="indexfile">Generate index file (<TT><a href="ndx.html">.ndx</a></TT> extension)</A></H3>
+<p>
By default, most GROMACS programs generate a set of index groups to select
the most common subsets of atoms from your system (e.g. Protein, Backbone,
C-alpha's, Solute, etc.).
program you would
<PRE>
% <a href="make_ndx.html">make_ndx</a> -f b4em
-</PRE>
+</PRE><p>
but don't bother for now.
<P><H3><A NAME="em">Perform an energy minimization of the peptide in solvent</A></H3>
-
+<p>
Now we have to perform an <EM>energy minimization</EM> of the
structure to remove the local strain in the peptide (due to generation
of hydrogen positions) and to remove bad Van der Waals contacts
the contents of this file
<PRE>
% more <a href="mdp_opt.html">em.mdp</a>
-</PRE>
+</PRE><p>
Preprocessing is done with the preprocessor called
<TT><a href="grompp.html">grompp</a></TT>. This reads
up the files just mentioned:
<PRE>
% <a href="grompp.html">grompp</a> -v -f em -c b4em -o em -p speptide
-</PRE>
+</PRE><p>
In this command the <tt>-v</tt> option turns on verbose mode, which
gives a little bit of clarifying info on what the program is doing.
We now have made a <EM>run input file</EM> (<TT><a href="tpr.html">em.tpr</a></TT>) which
we can do the energy minimization:
<PRE>
% <a href="mdrun.html">mdrun</a> -v -s em -o em -c after_em -g emlog
-</PRE>
+</PRE><p>
In this command the <tt>-v</tt> option turns on verbose mode again.
The <tt>-o</tt> option sets the filename for the trajectory file,
which is not very important in energy minimizations. The <tt>-c</tt>
<PRE>
STEEPEST DESCENTS converged to 2000
Potential Energy = -1.19482e+05
-</PRE>
+</PRE><p>
which means our criterium is met, and we can proceed to the next step.
<P><H3><A NAME="posres">
Perform a short MD run with position restraints on the peptide</A>
-</H3>
+</H3><p>
Position restrained MD means Molecular Dynamics in which a part of the
system is not allowed to move far off their starting positions. To be
able to run with position restraints we must add a section to the
#ifdef POSRES<BR>
#include "<a href="itp.html">posres.itp</a>"<BR>
#endif
-</PRE>
+</PRE><p>
In the <a href="top.html">topology file</a> we use
conditional inclusion, i.e. only if a variable <TT>POSRES</TT> is set
in the preprocessor do we include the file, this allows us to use the
At last we can generate the input for the position restrained mdrun:
<PRE>
% <a href="grompp.html">grompp</a> -f pr -o pr -c after_em -r after_em -p speptide
-</PRE>
+</PRE><p>
Now it's <a href="mdrun.html">MDrun</a> time:
<PRE>
% <a href="mdrun.html">mdrun</a> -v -s pr -e pr -o pr -c after_pr -g prlog >& pr.job &
-</PRE>
+</PRE><p>
This run is started in the background (it will take a while), you
can watch how long it will take by typing:
<PRE>
% tail -f pr.job
-</PRE>
+</PRE><p>
With the <tt>Ctrl-C</tt> key you can kill the <tt>tail</tt> command.
A good check of your simulation is to see whether density and potential
energies have converged:
<PRE>
% <a href="g_energy.html">g_energy</a> -f pr -o out -w
-</PRE>
+</PRE><p>
The <a href="g_energy.html">
g_energy</a> program will prompt you to select a number of energy terms
from a list. For potential energy type:
<PRE>
9 0
-</PRE>
+</PRE><p>
If you have the xmgr program installed it will automatically pop up on your
screen with the energy plot. You can do the same for the density
and other energy terms, such as Solvent-Protein interactions.
<P><H3><A NAME="full">Perform full MD without restraints</A></H3>
-Full MD is very similar to the restrained MD as far as GROMACS is
+<p>Full MD is very similar to the restrained MD as far as GROMACS is
concerned. Check out the <TT><a href="mdp_opt.html">full.mdp</a></TT> for details.
<PRE>
% <a href="grompp.html">grompp</a> -v -f full -o full -c after_pr -p speptide
-</PRE>
+</PRE><p>
Then we can start mdrunning
<PRE>
% <a href="mdrun.html">mdrun</a> -v -s full -e full -o full -c after_full -g flog >& full.job &
-</PRE>
+</PRE><p>
You should do similar convergence checks (and more!) as for the position
restrained simulation.
<P><H3><A NAME="analysis">Analysis</A></H3>
+<p>
We will not describe analysis in detail, because most analysis tools
are described in the Analysis chapter of the printed manual.
We just list a few of the possibilities within GROMACS. By now you should be
<br><hr><br>
-<P><H1><A NAME="you">Your own System.</A></H1>
+<P><H2><A NAME="you">Your own System</A></H2>
<P>
For proteins in water (or other solvent) the route is described above.
For other systemd (eg. pure liquids or mixtures) one needs:
</ul>
<br><hr><br>
-<P><H1><A NAME="info">More Info</A></h1>
+<P><H2><A NAME="info">More Info</A></h2>
<P>
More info can be found in the
<br><hr><br>
-<P><H1><A NAME="ref">References</A></h1>
+<P><H2><A NAME="ref">References</A></h2>
<blockquote>
<dl>
</dl>
</blockquote>
-<br><hr><br>
+<br>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
</BODY>
</HTML>
--- /dev/null
+<TITLE>gmxcheck</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>gmxcheck</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+gmxcheck reads a trajectory (<tt>.<a href="trj.html">trj</a></tt>, <tt>.<a href="trr.html">trr</a></tt> or
+<tt>.<a href="xtc.html">xtc</a></tt>) or an energy file (<tt>.<a href="ene.html">ene</a></tt> or <tt>.<a href="edr.html">edr</a></tt>)
+and prints out useful information about them.<p>
+Option <tt>-c</tt> checks for presence of coordinates,
+velocities and box in the file, for close contacts (smaller than
+<tt>-vdwfac</tt> and not bonded, i.e. not between <tt>-bonlo</tt>
+and <tt>-bonhi</tt>, all relative to the sum of both Van der Waals
+radii) and atoms outside the box (these may occur often and are
+no problem). If velocities are present, an estimated temperature
+will be calculated from them.<p>
+The program will compare run input (<tt>.<a href="tpr.html">tpr</a></tt>, <tt>.<a href="tpb.html">tpb</a></tt> or
+<tt>.<a href="tpa.html">tpa</a></tt>) files
+when both <tt>-s1</tt> and <tt>-s2</tt> are supplied.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f2</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s1</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> top1.tpr</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s2</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> top2.tpr</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-c</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input, Opt. </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> ener.edr</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic energy: <a href="edr.html">edr</a> <a href="ene.html">ene</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-e2</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> ener2.edr</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic energy: <a href="edr.html">edr</a> <a href="ene.html">ene</a> </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-vdwfac</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.8</tt> </TD><TD> Fraction of sum of VdW radii used as warning cutoff </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-bonlo</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.4</tt> </TD><TD> Min. fract. of sum of VdW radii for bonded atoms </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-bonhi</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.7</tt> </TD><TD> Max. fract. of sum of VdW radii for bonded atoms </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-tol</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Tolerance for comparing real values </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>gmxdump</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>gmxdump</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+gmxdump reads a run input file (<tt>.<a href="tpa.html">tpa</a></tt>/<tt>.<a href="tpr.html">tpr</a></tt>/<tt>.<a href="tpb.html">tpb</a></tt>),
+a trajectory (<tt>.<a href="trj.html">trj</a></tt>/<tt>.<a href="trr.html">trr</a></tt>/<tt>.<a href="xtc.html">xtc</a></tt>) or an energy
+file (<tt>.<a href="ene.html">ene</a></tt>/<tt>.<a href="edr.html">edr</a></tt>) and prints that to standard
+output in a readable format. This program is essential for
+checking your run input file in case of problems.<p>
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> ener.edr</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic energy: <a href="edr.html">edr</a> <a href="ene.html">ene</a> </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]nr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Show index numbers in output (leaving them out makes comparison easier, but creates a useless topology) </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
<title>gro file format</title>
-<body>
-<h1>gro file format</h1>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<h2>gro file format</h2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
<p>Files with the gro file extension contain a molecular structure in
Gromos87 format. gro files can be used as trajectory by simply
Note that this is the format for writing, as in the above example
fields may be written without spaces, and therefore can not be read
with the same format statement in C.
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
</body>
--- /dev/null
+<TITLE>grompp</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>grompp</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+The gromacs preprocessor
+reads a molecular topology file, checks the validity of the
+file, expands the topology from a molecular description to an atomic
+description. The topology file contains information about
+molecule types and the number of molecules, the preprocessor
+copies each molecule as needed.
+There is no limitation on the number of molecule types.
+Bonds and bond-angles can be converted into constraints, separately
+for hydrogens and heavy atoms.
+Then a coordinate file is read and velocities can be generated
+from a Maxwellian distribution if requested.
+grompp also reads parameters for the <a href="mdrun.html">mdrun</a>
+(eg. number of MD steps, time step, cut-off), and others such as
+NEMD parameters, which are corrected so that the net acceleration
+is zero.
+Eventually a binary file is produced that can serve as the sole input
+file for the MD program.<p>
+grompp calls the c-preprocessor to resolve includes, macros
+etcetera. To specify a macro-preprocessor other than /lib/cpp
+(such as m4)
+you can put a line in your parameter file specifying the path
+to that cpp. Specifying <tt>-pp</tt> will get the pre-processed
+topology file written out.<p>
+If your system does not have a c-preprocessor, you can still
+use grompp, but you do not have access to the features
+from the cpp. Command line options to the c-preprocessor can be given
+in the <tt>.<a href="mdp.html">mdp</a></tt> file. See your local manual (man cpp).<p>
+When using position restraints a file with restraint coordinates
+can be supplied with <tt>-r</tt>, otherwise constraining will be done
+relative to the conformation from the <tt>-c</tt> option.<p>
+Starting coordinates can be read from trajectory with <tt>-t</tt>.
+The last frame with coordinates and velocities will be read,
+unless the <tt>-time</tt> option is used.
+Note that these velocities will not be used when <tt>gen_vel = yes</tt>
+in your <tt>.<a href="mdp.html">mdp</a></tt> file. If you want to continue a crashed run, it is
+easier to use <tt><a href="tpbconv.html">tpbconv</a></tt>.<p>
+When preparing an input file for parallel <tt><a href="mdrun.html">mdrun</a></tt> it may
+be advantageous to partition the simulation system over the
+nodes in a way in which each node has a similar amount of
+work. The -shuffle option does just that. For a single protein
+in water this does not make a difference, however for a system where
+you have many copies of different molecules (e.g. liquid mixture
+or membrane/water system) the option is definitely a must.<p>
+A further optimization for parallel systems is the <tt>-sort</tt>
+option which sorts molecules according to coordinates. This must
+always be used in conjunction with <tt>-shuffle</tt>, however
+sorting also works when you have only one molecule type.<p>
+Using the <tt>-morse</tt> option grompp can convert the harmonic bonds
+in your topology to morse potentials. This makes it possible to break
+bonds. For this option to work you need an extra file in your $GMXLIB
+with dissociation energy. Use the -debug option to get more information
+on the workings of this option (look for MORSE in the grompp.log file
+using less or something like that).<p>
+By default all bonded interactions which have constant energy due to
+dummy atom constructions will be removed. If this constant energy is
+not zero, this will result in a shift in the total energy. All bonded
+interactions can be kept by turning off <tt>-rmdumbds</tt>. Additionally,
+all constraints for distances which will be constant anyway because
+of dummy atom constructions will be removed. If any constraints remain
+which involve dummy atoms, a fatal error will result.<p>To verify your run input file, please make notice of all warnings
+on the screen, and correct where necessary. Do also look at the contents
+of the <tt>mdout.<a href="mdp.html">mdp</a></tt> file, this contains comment lines, as well as
+the input that <tt>grompp</tt> has read. If in doubt you can start grompp
+with the <tt>-debug</tt> option which will give you more information
+in a file called grompp.log (along with real debug info). Finally, you
+can see the contents of the run input file with the <tt><a href="gmxdump.html">gmxdump</a></tt>
+program.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="mdp.html"> grompp.mdp</a></tt> </TD><TD> Input </TD><TD> grompp input file with MD parameters </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-po</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="mdp.html"> mdout.mdp</a></tt> </TD><TD> Output </TD><TD> grompp input file with MD parameters </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-c</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> conf.gro</a></tt> </TD><TD> Input </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-r</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> conf.gro</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-deshuf</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> deshuf.ndx</a></tt> </TD><TD> Output, Opt. </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-p</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="top.html"> topol.top</a></tt> </TD><TD> Input </TD><TD> Topology file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-pp</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="top.html">processed.top</a></tt> </TD><TD> Output, Opt. </TD><TD> Topology file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Output </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-t</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.trr</a></tt> </TD><TD> Input, Opt. </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]v</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Be loud and noisy </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-time</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Take frame at or first after this time. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-np</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Generate statusfile for # nodes </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]shuffle</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Shuffle molecules over nodes </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]sort</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Sort molecules according to X coordinate </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]rmdumbds</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Remove constant bonded interactions with dummies </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-load</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Releative load capacity of each node on a parallel machine. Be sure to use quotes around the string, which should contain a number for each node </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-maxwarn</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>10</tt> </TD><TD> Number of warnings after which input processing stops </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]check14</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Remove 1-4 interactions without Van der Waals </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
<title>hat file format</title>
-<body>
-<h1>hat file format</h1>
-<h2>Description</h2>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<h2>hat file format</h2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<h3>Description</h3>
Files with the hat file extension contain
a fourier transform of a spread function used in the PPPM algorithm.
Eigenvectors are produced by <a href="mk_ghat.html">mk_ghat</a>
and read by <a href="mdrun.html">mdrun</a>.
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
</body>
--- /dev/null
+<TITLE>highway</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>highway</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+highway is the gromacs highway simulator. It is an X-windows
+gadget that shows a (periodic) autobahn with a user defined
+number of cars. Fog can be turned on or off to increase the
+number of crashes. Nice for a background CPU-eater
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="dat.html"> highway.dat</a></tt> </TD><TD> Input </TD><TD> Generic data file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-a</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="dat.html"> auto.dat</a></tt> </TD><TD> Input </TD><TD> Generic data file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
<title>itp file format</title>
-<body>
-<h1>itp file format</h1>
-<h2>Description</h2>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<h2>itp file format</h2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<h3>Description</h3>
The itp file extension stands for include toplogy. These files are included in topology files ( with the <a href="top.html"><tt>top</tt></a> extension )
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
</body>
<title>log file format</title>
-<body>
-<h1>log file format</h1>
-<h2>Description</h2>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<h2>log file format</h2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<h3>Description</h3>
Logfiles are generated by some GROMACS programs and are usually in
human-readable format. Use <tt>more logfile</tt>.
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
</body>
<title>m2p file format</title>
-<body>
-<h1>m2p file format</h1>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<h2>m2p file format</h2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<h3>Description</h3>
The m2p file format contains input options for the
<a href="xpm2ps.html">xpm2ps</a> program. All of these options
are very easy to comprehend when you look at the PosScript(tm) output
y-tickfontsize = 10
y-tickfont = Helvetica
</pre>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
</body>
--- /dev/null
+<TITLE>make_ndx</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>make_ndx</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+Index groups are necessary for almost every gromacs program.
+All these programs can generate default index groups. You ONLY
+have to use make_<a href="ndx.html">ndx</a> when you need SPECIAL index groups.
+There is a default index group for the whole system, 9 default
+index groups are generated for proteins, a default index group
+is generated for every other residue name.<p>When no index file is supplied, also make_<a href="ndx.html">ndx</a> will generate the
+default groups.
+With the index editor you can select on atom, residue and chain names
+and numbers, you can use NOT, AND and OR, you can split groups
+into chains, residues or atoms. You can delete and rename groups.<p>
+The atom numbering in the editor and the index file starts at 1.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> conf.gro</a></tt> </TD><TD> Input </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Output </TD><TD> Index file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
<title>map file format</title>
-<body>
-<h1>map file format</h1>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<h2>map file format</h2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
This file maps matrix data to RGB values which is used by the
<a href="do_dssp.html">do_dssp</a> program.<p>
The format of this file is as follow: first line number of elements
G 3-Helix 1.0 0.0 1.0
I 5-Helix 1.0 0.6 0.0
</pre>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
</body>
<title>mdp file format</title>
-<body>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
<h2>mdp file format</h2>
-
-<P> <a href="mdp_opt.html">full description of the options</a>. </P>
-
-<P> Here is a sample mdp file.
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<P> Follow <a href="mdp_opt.html">this link</a> for a detailed description of the options</a>. </P>
+
+<P> Below is a sample mdp file.
The ordering of the items is not important, but if you enter the same
thing twice, the <b>first</b> is used. Dashes and underscores on the
left hand side are ignored.</P>
</pre>
<hr>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
</body>
<HTML>
<TITLE>mdp options</TITLE>
-<BODY>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
<!--
-->
-<h1>mdp options</h1>
-
-<IMG SRC="../gif/rainbow.gif" WIDTH=100% HEIGHT=7>
-<P>
-
-<H3>Table of Contents:</H3>
+<h2>mdp options</h2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Table of Contents</H3>
<ul>
<li><A HREF="#general"><b>General remarks</b></A>
</ul>
</P>
-<IMG SRC="../gif/rainbow.gif" WIDTH=100% HEIGHT=7>
+<HR>
<A NAME="general"><br>
<h3>General</h3>
<A HREF="#sa">zero_temp_time</A><br>
</multicol>
-<IMG SRC="../gif/rainbow.gif" WIDTH=100% HEIGHT=7>
-<P>
-
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
</BODY>
</HTML>
--- /dev/null
+<TITLE>mdrun</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>mdrun</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+The mdrun program performs Molecular Dynamics simulations.
+It reads the run input file (<tt>-s</tt>) and distributes the
+topology over nodes if needed. The coordinates are passed
+around, so that computations can begin.
+First a neighborlist is made, then the forces are computed.
+The forces are globally summed, and the velocities and
+positions are updated. If necessary shake is performed to constrain
+bond lengths and/or bond angles.
+Temperature and Pressure can be controlled using weak coupling to a
+bath.<p>
+mdrun produces at least three output file, plus one log file
+(<tt>-g</tt>) per node.
+The trajectory file (<tt>-o</tt>), contains coordinates, velocities and
+optionally forces.
+The structure file (<tt>-c</tt>) contains the coordinates and
+velocities of the last step.
+The energy file (<tt>-e</tt>) contains energies, the temperature,
+pressure, etc, a lot of these things are also printed in the log file
+of node 0.
+Optionally coordinates can be written to a compressed trajectory file
+(<tt>-x</tt>).<p>
+When running in parallel with PVM or an old version of MPI the
+<tt>-np</tt> option must be given to indicate the number of
+nodes.<p>
+The option <tt>-dgdl</tt> is only used when free energy perturbation is
+turned on.<p>
+With <tt>-rerun</tt> an input trajectory can be given for which
+forces and energies will be (re)calculated. Neighbor searching will be
+performed for every frame, unless <tt>nstlist</tt> is zero
+(see the <tt>.<a href="mdp.html">mdp</a></tt> file).<p>
+ED (essential dynamics) sampling is switched on by using the <tt>-ei</tt>
+flag followed by an <tt>.<a href="edi.html">edi</a></tt> file.
+The <tt>.<a href="edi.html">edi</a></tt> file can be produced using options in the essdyn
+menu of the WHAT IF program. mdrun produces a <tt>.<a href="edo.html">edo</a></tt> file that
+contains projections of positions, velocities and forces onto selected
+eigenvectors.<p>
+The -table option can be used to pass mdrun a formatted table with
+user-defined potential functions. The file is read from either the
+current directory or from the GMXLIB directory. A number of preformatted
+tables are presented in the GMXLIB dir, for 6-8, 6-9, 6-10, 6-11, 6-12
+Lennard Jones potentials with normal Coulomb.<p>
+The options <tt>-pi</tt>, <tt>-po</tt>, <tt>-pd</tt>, <tt>-pn</tt> are used
+for potential of mean force calculations and umbrella sampling.
+See manual.<p>
+When mdrun receives a TERM signal, it will set nsteps to the current
+step plus one. When mdrun receives a USR1 signal, it will set nsteps
+to the next multiple of nstxout after the current step.
+In both cases all the usual output will be written to file.
+When running with MPI, a signal to one of the mdrun processes
+is sufficient, this signal should not be sent to mpirun or
+the mdrun process that is the parent of the others.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.trr</a></tt> </TD><TD> Output </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-x</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xtc.html"> traj.xtc</a></tt> </TD><TD> Output, Opt. </TD><TD> Compressed trajectory (portable xdr format) </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-c</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> confout.gro</a></tt> </TD><TD> Output </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> ener.edr</a></tt> </TD><TD> Output </TD><TD> Generic energy: <a href="edr.html">edr</a> <a href="ene.html">ene</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-g</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html"> md.log</a></tt> </TD><TD> Output </TD><TD> Log file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-dgdl</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> dgdl.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-table</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> table.xvg</a></tt> </TD><TD> Input, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-rerun</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> rerun.xtc</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-ei</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="edi.html"> sam.edi</a></tt> </TD><TD> Input, Opt. </TD><TD> ED sampling input </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-eo</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="edo.html"> sam.edo</a></tt> </TD><TD> Output, Opt. </TD><TD> ED sampling output </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-pi</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ppa.html"> pull.ppa</a></tt> </TD><TD> Input, Opt. </TD><TD> Pull parameters </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-po</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ppa.html"> pullout.ppa</a></tt> </TD><TD> Output, Opt. </TD><TD> Pull parameters </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-pd</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="pdo.html"> pull.pdo</a></tt> </TD><TD> Output, Opt. </TD><TD> Pull data output </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-pn</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> pull.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-deffnm</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Set the default filename for all file options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]v</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Be loud and noisy </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]compact</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Write a compact log file </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>mk_angndx</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>mk_angndx</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+mk_angndx makes an index file for calculation of
+angle distributions etc. It uses a run input file (<tt>.tpx</tt>) for the
+definitions of the angles, dihedrals etc.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> angle.ndx</a></tt> </TD><TD> Output </TD><TD> Index file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-type</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>angle</tt> </TD><TD> Type of angle: angle, <a href="g96.html">g96</a>-angle, dihedral, improper, ryckaert-bellemans or phi-psi </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
<title>mtx file format</title>
-<body>
-<h1>mtx file format</h1>
-<h2>Description</h2>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<h2>mtx file format</h2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
Files with the mtx file extension contain a matrix.
The file format is identical to the <a href="trj.html">trj</a> format.
Currently this file format is only used for hessian matrices,
which are produced with <a href="nmrun.html">nmrun</a> and read by
<a href="g_nmeig.html">g_nmeig</a>.
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
</body>
<title>ndx file format</title>
-<body>
-<h1>ndx file format</h1>
-<h2>Description</h2>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<h2>ndx file format</h2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
The GROMACS index file (usually called index.ndx) contains some
user definable sets of atoms. The file can be read by
most analysis programs, by the graphics program (<a href=ngmx.html>ngmx</a>)
The second group <b>Hydrogen</b> has 6 elements.
<p>
An index file generation tool is available: <a href=make_ndx.html>make_ndx</a>.
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
</body>
--- /dev/null
+<TITLE>ngmx</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>ngmx</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+ngmx is the Gromacs trajectory viewer. This program reads a
+trajectory file, a run input file and an index file and plots a
+3D structure of your molecule on your standard X Window
+screen. No need for a high end graphics workstation, it even
+works on Monochrome screens.<p>
+The following features have been implemented:
+3D view, rotation, translation and scaling of your molecule(s),
+labels on atoms, animation of trajectories,
+hardcopy in PostScript format, user defined atom-filters
+runs on MIT-X (real X), open windows and motif,
+user friendly menus, option to remove periodicity, option to
+show computational box.<p>
+Some of the more common X command line options can be used:<br>
+-bg, -fg change colors, -font fontname, changes the font.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+</TABLE>
+<P>
+<H3>Diagnostics</H3>
+<UL>
+<LI>Balls option does not work
+<LI>Some times dumps core without a good reason
+</UL>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>nmrun</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>nmrun</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+nmrun builds a Hessian matrix from single conformation.
+For usual Normal Modes-like calculations, make sure that
+the structure provided is properly energy-minimised.
+The generated matrix can be diagonalized by <a href="g_nmeig.html">g_nmeig</a>.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-m</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="mtx.html"> hessian.mtx</a></tt> </TD><TD> Output </TD><TD> Hessian matrix </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-g</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html"> nm.log</a></tt> </TD><TD> Output </TD><TD> Log file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]v</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Verbose mode </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]compact</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Write a compact log file </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
<title>out file format</title>
-<body>
-<h1>out file format</h1>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<h2>out file format</h2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
Files with the out file extension contain generic output. As it is not possible
to categorise all data file formats, GROMACS has a generic file format called
out of which no format is given.
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
</body>
<title>pdb file format</title>
-<body>
-<h1>pdb file format</h1>
-<h2>Description</h2>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<h2>pdb file format</h2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
Files with the <a href="pdb.html">.pdb</a> extension are molecular
structure files in the protein databank file format. The protein
can be found on the <A HREF="../links.html">Links page</A>.
<p>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
</body>
--- /dev/null
+<TITLE>pdb2gmx</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>pdb2gmx</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+This program reads a <a href="pdb.html">pdb</a> file, lets you choose a forcefield, reads
+some database files, adds hydrogens to the molecules and generates
+coordinates in Gromacs (Gromos) format and a topology in Gromacs format.
+These files can subsequently be processed to generate a run input file.
+<p>
+Note that a <a href="pdb.html">pdb</a> file is nothing more than a file format, and it
+need not necessarily contain a protein structure. Every kind of
+molecule for which there is support in the database can be converted.
+If there is no support in the database, you can add it yourself.<p>
+The program has limited intelligence, it reads a number of database
+files, that allow it to make special bonds (Cys-Cys, Heme-His, etc.),
+if necessary this can be done manually. The program can prompt the
+user to select which kind of LYS, ASP, GLU, CYS or HIS residue she
+wants. For LYS the choice is between LYS (two protons on NZ) or LYSH
+(three protons, default), for ASP and GLU unprotonated (default) or
+protonated, for HIS the proton can be either on ND1 (HISA), on NE2
+(HISB) or on both (HISH). By default these selections are done
+automatically. For His, this is based on an optimal hydrogen bonding
+conformation. Hydrogen bonds are defined based on a simple geometric
+criterium, specified by the maximum hydrogen-donor-acceptor angle
+and donor-acceptor distance, which are set by <tt>-angle</tt> and
+<tt>-dist</tt> respectively.<p>
+Option <tt>-merge</tt> will ask if you want to merge consecutive chains
+into one molecule, this can be useful for connecting chains with a
+disulfide brigde.<p>
+pdb2gmx will also check the occupancy field of the <a href="pdb.html">pdb</a> file.
+If any of the occupanccies are not one, indicating that the atom is
+not resolved well in the structure, a warning message is issued.
+When a <a href="pdb.html">pdb</a> file does not originate from an X-Ray structure determination
+all occupancy fields may be zero. Either way, it is up to the user
+to verify the correctness of the input data (read the article!).<p>
+During processing the atoms will be reordered according to Gromacs
+conventions. With <tt>-n</tt> an index file can be generated that
+contains one group reordered in the same way. This allows you to
+convert a Gromos trajectory and coordinate file to Gromos. There is
+one limitation: reordering is done after the hydrogens are stripped
+from the input and before new hydrogens are added. This means that
+you should not use <tt>-ignh</tt>.<p>
+The <tt>.<a href="gro.html">gro</a></tt> and <tt>.<a href="g96.html">g96</a></tt> file formats do not support chain
+identifiers. Therefore it is useful to enter a <a href="pdb.html">pdb</a> file name at
+the <tt>-o</tt> option when you want to convert a multichain <a href="pdb.html">pdb</a> file.
+<p>
+<tt>-sort</tt> will sort all residues according to the order in the
+database, sometimes this is necessary to get charge groups
+together.<p>
+<tt>-alldih</tt> will generate all proper dihedrals instead of only
+those with as few hydrogens as possible, this is useful for use with
+the Charmm forcefield.<p>
+The option <tt>-dummy</tt> removes hydrogen and fast improper dihedral
+motions. Angular and out-of-plane motions can be removed by changing
+hydrogens into dummy atoms and fixing angles, which fixes their
+position relative to neighboring atoms. Additionally, all atoms in the
+aromatic rings of the standard amino acids (i.e. PHE, TRP, TYR and HIS)
+can be converted into dummy atoms, elminating the fast improper dihedral
+fluctuations in these rings. Note that in this case all other hydrogen
+atoms are also converted to dummy atoms. The mass of all atoms that are
+converted into dummy atoms, is added to the heavy atoms.<p>
+Also slowing down of dihedral motion can be done with <tt>-heavyh</tt>
+done by increasing the hydrogen-mass by a factor of 4. This is also
+done for water hydrogens to slow down the rotational motion of water.
+The increase in mass of the hydrogens is subtracted from the bonded
+(heavy) atom so that the total mass of the system remains the same.
+Reference Feenstra et al., J. Comput. Chem. 20, 786 (1999).
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> eiwit.pdb</a></tt> </TD><TD> Input </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> conf.gro</a></tt> </TD><TD> Output </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-p</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="top.html"> topol.top</a></tt> </TD><TD> Output </TD><TD> Topology file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-i</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="itp.html"> posre.itp</a></tt> </TD><TD> Output </TD><TD> Include file for topology </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> clean.ndx</a></tt> </TD><TD> Output, Opt. </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-q</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> clean.pdb</a></tt> </TD><TD> Output, Opt. </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]merge</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Merge multiple chains into one molecule </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]inter</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Set the next 6 options to interactive </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]ss</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Interactive SS bridge selection </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]ter</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Interactive termini selection, iso charged </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]lys</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Interactive Lysine selection, iso charged </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]asp</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Interactive Aspartic Acid selection, iso charged </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]glu</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Interactive Glutamic Acid selection, iso charged </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]his</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Interactive Histidine selection, iso checking H-bonds </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-angle</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 135</tt> </TD><TD> Minimum hydrogen-donor-acceptor angle for a H-bond (degrees) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dist</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.3</tt> </TD><TD> Maximum donor-acceptor distance for a H-bond (nm) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]una</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Select aromatic rings with united CH atoms on Phenylalanine, Tryptophane and Tyrosine </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]sort</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Sort the residues according to database </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]H14</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use 1-4 interactions between hydrogen atoms </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]ignh</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Ignore hydrogen atoms that are in the <a href="pdb.html">pdb</a> file </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]alldih</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Generate all proper dihedrals </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dummy</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Convert atoms to dummy atoms: none, hydrogens or aromatics </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]heavyh</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Make hydrogen atoms heavy </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]deuterate</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Change the mass of hydrogens to 2 amu </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>protonate</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>protonate</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+<tt>protonate</tt> reads (a) conformation(s) and adds all missing
+hydrogens as defined in <tt>ffgmx2.<a href="hdb.html">hdb</a></tt>. If only <tt>-s</tt> is
+specified, this conformation will be protonated, if also <tt>-f</tt>
+is specified, the conformation(s) will be read from this file
+which can be either a single conformation or a trajectory.
+<p>
+If a <a href="pdb.html">pdb</a> file is supplied, residue names might not correspond to
+to the GROMACS naming conventions, in which case these residues will
+probably not be properly protonated.
+<p>
+If an index file is specified, please note that the atom numbers
+should correspond to the <b>protonated</b> state.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">protonated.xtc</a></tt> </TD><TD> Output </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
<title>rtp file format</title>
-<body>
-<h1>rtp file format</h1>
-<h2>Description</h2>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<h2>rtp file format</h2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
The rtp file extension stands for residue toplogy.
Such a file is needed by <a href="pdb2gmx.html">pdb2gmx</a>
to make a GROMACS topology for a protein contained in a <tt>.pdb</tt>
[ atoms ]
ZN ZN 2.000 0
</PRE>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
</body>
--- /dev/null
+P { text-indent: 0em; font-family: helvetica,verdana,arial,sans-serif }
+H1 { text-indent: 0em; font-size: 24pt; font-family: serif }
+H2 { text-indent: 0em; font-size: 24pt; font-weight: bold; font-family: helvetica,verdana,arial,sans-serif }
+H3 { text-indent: 0em; font-size: 18pt; font-weight: bold; font-family: helvetica,verdana,arial,sans-serif }
+A:link { text-decoration: none; font-family: helvetica,verdana,arial,sans-serif }
+A:active { text-decoration: none; font-family: helvetica,verdana,arial,sans-serif }
+A:visited { text-decoration: none; font-family: helvetica,verdana,arial,sans-serif }
+body { text-indent: 0em; font-family: helvetica,verdana,arial,sans-serif }
+td { font-family: helvetica,verdana,arial,sans-serif }
+th { font-family: helvetica,verdana,arial,sans-serif }
<title>tex file format</title>
-<body>
-<h1>tex file format</h1>
-<h2>Description</h2>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<h2>tex file format</h2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
We use <b>LaTeX</b> for <i>document</i> processing.
Although the input is not so
user friendly, it has some advantages over <i>word</i> processors.
<li> It makes anything from letters to a thesis
<li> Much more...
</ul>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
</body>
<title>top file format</title>
-<body>
-<h1>top file format</h1>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<h2>top file format</h2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
The top file extension stands for topology. It is an ascii file which is
read by <a href="grompp.html">grompp</a> which processes it
and creates a binary topology (<a href="tpb.html">tpb-file</a>).<br>
Urea 1
SOL 1000
</pre>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
</body>
<title>tpa file format</title>
-<body>
-<h1>tpa file format</h1>
-<h2>Description</h2>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<h2>tpa file format</h2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
The tpa file extension stands for binary run input file. This file contains
the starting structure of your simulation, The molecular topology and
all the simulation data. Because this file is in binary format it
<pre>
% <a href="gmxcheck.html">gmxcheck</a> -s1 top1 -s2 top2 | more
</pre>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
</body>
<title>tpb file format</title>
-<body>
-<h1>tpb file format</h1>
-<h2>Description</h2>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<h2>tpb file format</h2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<h3>Description</h3>
The tpb file extension stands for binary run input file. This file contains
the starting structure of your simulation, The molecular topology and
all the simulation data. Because this file is in binary format it
<pre>
% <a href="gmxcheck.html">gmxcheck</a> -s1 top1 -s2 top2 | more
</pre>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
</body>
--- /dev/null
+<TITLE>tpbconv</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>tpbconv</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+tpbconv can edit run input files in two ways.<p><b>1st.</b> by creating a run input file
+for a continuation run when your simulation has crashed due to e.g.
+a full disk, or by making a continuation run input file.
+Note that a frame with coordinates and velocities is needed,
+which means that when you never write velocities, you can not use
+tpbconv and you have to start the run again from the beginning.<p>
+<b>2nd.</b> by creating a tpx file for a subset of your original
+tpx file, which is useful when you want to remove the solvent from
+your tpx file, or when you want to make e.g. a pure Ca tpx file.
+<b>WARNING: this tpx file is not fully functional</b>.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.trr</a></tt> </TD><TD> Input, Opt. </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> tpxout.tpr</a></tt> </TD><TD> Output </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-time</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Continue from frame at this time (ps) instead of the last frame </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-extend</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Extend runtime by this amount (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-until</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Extend runtime until this ending time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]unconstrained</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> For a continuous trajectory, the constraints should not be solved before the first step (default) </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
<title>tpr file format</title>
-<body>
-<h1>tpr file format</h1>
-<h2>Description</h2>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<h2>tpr file format</h2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<h3>Description</h3>
The tpr file extension stands for portable binary run input file. This file
contains the starting structure of your simulation, the molecular topology
and all the simulation parameters. Because this file is in binary format it
<pre>
<a href="gmxcheck.html">gmxcheck</a> -s1 top1 -s2 top2 | more
</pre>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
</body>
<title>trj file format</title>
-<body>
-<h1>trj file format</h1>
-<h2>Description</h2>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<h2>trj file format</h2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<h3>Description</h3>
Files with the trj file extension contain the trajectory of a simulation.
In this file all the coordinates, velocities, forces and energies are
printed as you told GROMACS in your mdp file. This file is in binary
<PRE>
% <a href="gmxcheck.html">gmxcheck</a> -f traj.trj
</PRE>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
</body>
--- /dev/null
+<TITLE>trjcat</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>trjcat</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+trjcat concatenates several input trajectory files in sorted order.
+In case of double time frames the one in the later file is used.
+By specifying <tt>-settime</tt> you will be asked for the start time
+of each file. The input files are taken from the command line,
+such that a command like <tt>trjcat -o fixed.<a href="trr.html">trr</a> *.<a href="trr.html">trr</a></tt> should do
+the trick.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> trajout.xtc</a></tt> </TD><TD> Output </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First time to use </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last time to use </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only write frame when t MOD dt = first time </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-prec</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>3</tt> </TD><TD> Precision for .<a href="xtc.html">xtc</a> and .<a href="gro.html">gro</a> writing in number of decimal places </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]vel</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Read and write velocities if possible </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]settime</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Change starting time interactively </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]sort</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Sort trajectory files (not frames) </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>trjconv</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>trjconv</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+trjconv can convert trajectory files in many ways:<br>
+<b>1.</b> from one format to another<br>
+<b>2.</b> select a subset of atoms<br>
+<b>3.</b> remove periodicity from molecules<br>
+<b>4.</b> keep multimeric molecules together<br>
+<b>5.</b> center atoms in the box<br>
+<b>6.</b> fit atoms to reference structure<br>
+<b>7.</b> reduce the number of frames<br>
+<b>8.</b> change the timestamps of the frames
+(<tt>-t0</tt> and <tt>-timestep</tt>)
+<p>
+The program <tt><a href="trjcat.html">trjcat</a></tt> can concatenate multiple trajectory files.
+<p>
+Currently seven formats are supported for input and output:
+<tt>.<a href="xtc.html">xtc</a></tt>, <tt>.<a href="trr.html">trr</a></tt>, <tt>.<a href="trj.html">trj</a></tt>, <tt>.<a href="gro.html">gro</a></tt>, <tt>.<a href="g96.html">g96</a></tt>,
+<tt>.<a href="pdb.html">pdb</a></tt> and <tt>.<a href="g87.html">g87</a></tt>.
+The file formats are detected from the file extension.
+The precision of <tt>.<a href="xtc.html">xtc</a></tt> and <tt>.<a href="gro.html">gro</a></tt> output is taken from the
+input file for <tt>.<a href="xtc.html">xtc</a></tt>, <tt>.<a href="gro.html">gro</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt>,
+and from the <tt>-ndec</tt> option for other input formats. The precision
+is always taken from <tt>-ndec</tt>, when this option is set.
+All other formats have fixed precision. <tt>.<a href="trr.html">trr</a></tt> and <tt>.<a href="trj.html">trj</a></tt>
+output can be single or double precision, depending on the precision
+of the trjconv binary.
+Note that velocities are only supported in
+<tt>.<a href="trr.html">trr</a></tt>, <tt>.<a href="trj.html">trj</a></tt>, <tt>.<a href="gro.html">gro</a></tt> and <tt>.<a href="g96.html">g96</a></tt> files.<p>
+Option <tt>-app</tt> can be used to
+append output to an existing trajectory file.
+No checks are performed to ensure integrity
+of the resulting combined trajectory file.
+<tt>.<a href="pdb.html">pdb</a></tt> files with all frames concatenated can be viewed with
+<tt>rasmol -nmrpdb</tt>.<p>
+It is possible to select part of your trajectory and write it out
+to a new trajectory file in order to save disk space, e.g. for leaving
+out the water from a trajectory of a protein in water.
+<b>ALWAYS</b> put the original trajectory on tape!
+We recommend to use the portable <tt>.<a href="xtc.html">xtc</a></tt> format for your analysis
+to save disk space and to have portable files.<p>
+There are two options for fitting the trajectory to a reference
+either for essential dynamics analysis or for whatever.
+The first option is just plain fitting to a reference structure
+in the structure file, the second option is a progressive fit
+in which the first timeframe is fitted to the reference structure
+in the structure file to obtain and each subsequent timeframe is
+fitted to the previously fitted structure. This way a continuous
+trajectory is generated, which might not be the case when using the
+regular fit method, e.g. when your protein undergoes large
+conformational transitions.<p>
+Option <tt>-pbc</tt> sets the type of periodic boundary condition
+treatment. <tt>whole</tt> puts the atoms in the box and then makes
+broken molecules whole (a run input file is required).
+<tt>inbox</tt> puts all the atoms in the box.
+<tt>nojump</tt> checks if atoms jump across the box and then puts
+them back. This has the effect that all molecules
+will remain whole (provided they were whole in the initial
+conformation), note that this ensures a continuous trajectory but
+molecules may diffuse out of the box. The starting configuration
+for this procedure is taken from the structure file, if one is
+supplied, otherwise it is the first frame.
+<tt>-pbc</tt> is ignored when <tt>-fit</tt> of <tt>-pfit</tt> is set,
+in that case molecules will be made whole.<p>
+Option <tt>-ur</tt> sets the unit cell representation for options
+<tt>whole</tt> and <tt>inbox</tt> of <tt>-pbc</tt>.
+All three options give different results for triclinc boxes and
+identical results for rectangular boxes.
+<tt>rect</tt> is the ordinary brick shape.
+<tt>tric</tt> is the triclinic unit cell.
+<tt>compact</tt> puts all atoms at the closest distance from the center
+of the box. This can be useful for visualizing e.g. truncated
+octahedrons.<p>
+Option <tt>-center</tt> centers the system in the box. The user can
+select the group which is used to determine the geometrical center.
+Use option <tt>-pbc whole</tt> in addition to <tt>-center</tt> when you
+want all molecules in the box after the centering.<p>
+With <tt>-dt</tt> it is possible to reduce the number of
+frames in the output. This option relies on the accuracy of the times
+in your input trajectory, so if these are inaccurate use the
+<tt>-timestep</tt>
+option to modify the time (this can be done simultaneously).<p>
+Using <tt>-trunc</tt> trjconv can truncate <tt>.<a href="trj.html">trj</a></tt> in place, i.e.
+without copying the file. This is useful when a run has crashed
+during disk I/O (one more disk full), or when two contiguous
+trajectories must be concatenated without have double frames.<p>
+<tt><a href="trjcat.html">trjcat</a></tt> is more suitable for concatenating trajectory files.<p>
+Option <tt>-dump</tt> can be used to extract a frame at or near
+one specific time from your trajectory.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> trajout.xtc</a></tt> </TD><TD> Output </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input, Opt. </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-fr</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> frames.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: ps, fs, ns, us, ms, s, m or h </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-skip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Only write every nr-th frame </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only write frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dump</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Dump frame nearest specified time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-t0</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Starting time (ps) (default: don't change) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-timestep</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Change time step between input frames (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-pbc</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> PBC treatment: none, whole, inbox or nojump </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ur</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>rect</tt> </TD><TD> Unit-cell representation: rect, tric or compact </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]center</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Center atoms in box </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-box</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 0</tt> </TD><TD> Size for new cubic box (default: read from input) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-shift</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 0</tt> </TD><TD> All coordinates will be shifted by framenr*shift </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]fit</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Fit molecule to ref structure in the structure file </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]pfit</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Progressive fit, to the previous fitted structure </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ndec</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>3</tt> </TD><TD> Precision for .<a href="xtc.html">xtc</a> and .<a href="gro.html">gro</a> writing in number of decimal places </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]vel</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Read and write velocities if possible </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]force</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Read and write forces if possible </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-trunc</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Truncate input <a href="trj.html">trj</a> file after this time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-exec</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Execute command for every output frame with the frame number as argument </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]app</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Append output </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]sep</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Write each frame to a separate .<a href="gro.html">gro</a> or .<a href="pdb.html">pdb</a> file </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>trjorder</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>trjorder</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+trjorder orders molecules according to the smallest distance
+to atoms in a reference group. It will ask for a group of reference
+atoms and a group of molecules. For each frame of the trajectory
+the selected molecules will be reordered according to the shortest
+distance between atom number <tt>-da</tt> in the molecule and all the
+atoms in the reference group. All atoms in the trajectory are written
+to the output trajectory.<p>
+trjorder can be useful for e.g. analyzing the n waters closest to a
+protein.
+In that case the reference group would be the protein and the group
+of molecules would consist of all the water atoms. When an index group
+of the first n waters is made, the ordered trajectory can be used
+with any Gromacs program to analyze the n closest waters.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> ordered.xtc</a></tt> </TD><TD> Output </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-na</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>3</tt> </TD><TD> Number of atoms in a molecule </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-da</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Atom used for the distance calculation </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
<title>trr file format</title>
-<body>
-<h1>trr file format</h1>
-<h2>Description</h2>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<h2>trr file format</h2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<h3>Description</h3>
Files with the trr file extension contain the trajectory of a simulation.
In this file all the coordinates, velocities, forces and energies are
printed as you told GROMACS in your mdp file. This file is in portable binary
<PRE>
% <a href="gmxcheck.html">gmxcheck</a> -f traj.trr
</PRE>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
</body>
--- /dev/null
+<TITLE>wheel</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>wheel</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+wheel plots a helical wheel representation of your sequence.The input sequence is in the .<a href="dat.html">dat</a> file where the first line contains
+the number of residues and each consecutive line contains a residuename.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="dat.html"> nnnice.dat</a></tt> </TD><TD> Input </TD><TD> Generic data file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="eps.html"> plot.eps</a></tt> </TD><TD> Output </TD><TD> Encapsulated PostScript (tm) file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-r0</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> The first residue number in the sequence </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-rot0</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Rotate around an angle initially (90 degrees makes sense) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-T</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Plot a title in the center of the wheel (must be shorter than 10 characters, or it will overwrite the wheel) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]nn</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Toggle numbers </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>x2top</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>x2top</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+x2top generates a primitive topology from a coordinate file.
+The program assumes all hydrogens are present when defining
+the hybridization from the atom name and the number of bonds.
+The program can also make an <a href="rtp.html">rtp</a> entry, which you can then add
+to the <a href="rtp.html">rtp</a> database.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> conf.gro</a></tt> </TD><TD> Input </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="top.html"> out.top</a></tt> </TD><TD> Output, Opt. </TD><TD> Topology file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-r</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="rtp.html"> out.rtp</a></tt> </TD><TD> Output, Opt. </TD><TD> Residue Type file used by <a href="pdb2gmx.html">pdb2gmx</a> </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-kb</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>400000</tt> </TD><TD> Bonded force constant (kJ/mol/nm^2) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-kt</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 400</tt> </TD><TD> Angle force constant (kJ/mol/rad^2) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-kp</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 5</tt> </TD><TD> Dihedral angle force constant (kJ/mol/rad^2) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nexcl</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>3</tt> </TD><TD> Number of exclusions </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]H14</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use 3rd neighbour interactions for hydrogen atoms </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]alldih</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Generate all proper dihedrals </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]round</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Round off measured values </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]pairs</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Output 1-4 interactions (pairs) in topology file </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-name</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>ICE</tt> </TD><TD> Name of your molecule </TD></TD>
+</TABLE>
+<P>
+<H3>Diagnostics</H3>
+<UL>
+<LI>The atom type selection is primitive. Virtually no chemical knowledge is used
+<LI>Periodic boundary conditions screw up the bonding
+<LI>No improper dihedrals are generated
+<LI>The atoms to atomtype translation table is incomplete (ffG43a1.n2t file in the $GMXLIB directory). Please extend it and send the results back to the GROMACS crew.
+</UL>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
<title>xpm file format</title>
-<body>
-<h1>xpm file format</h1>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<h2>xpm file format</h2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
The GROMACS xpm file format is compatible with the XPixMap format
and is used for storing matrix data.
Thus GROMACS xpm files can be viewed directly with programs like XV.
"DACCDDDDDDEEE",
"ADEEEEEEEFFFF"
</pre>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
</body>
--- /dev/null
+<TITLE>xpm2ps</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>xpm2ps</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+xpm2ps makes a beautiful color plot of an XPixelMap file.
+Labels and axis can be displayed, when they are supplied
+in the correct matrix format.
+Matrix data may be generated by programs such as <a href="do_dssp.html">do_dssp</a>, <a href="g_rms.html">g_rms</a> or
+<a href="g_mdmat.html">g_mdmat</a>.<p>
+Parameters are set in the <tt><a href="m2p.html">m2p</a></tt> file optionally supplied with
+<tt>-di</tt>. Reasonable defaults are provided. Settings for the y-axis
+default to those for the x-axis. Font names have a defaulting hierarchy:
+titlefont -> legendfont; titlefont -> (xfont -> yfont -> ytickfont)
+-> xtickfont, e.g. setting titlefont sets all fonts, setting xfont
+sets yfont, ytickfont and xtickfont.<p>
+With <tt>-f2</tt> a 2nd matrix file can be supplied, both matrix
+files will be read simultaneously and the upper left half of the
+first one (<tt>-f</tt>) is plotted together with the lower right
+half of the second one (<tt>-f2</tt>). The diagonal will contain
+values from the matrix file selected with <tt>-diag</tt>.
+Plotting of the diagonal values can be suppressed altogether by
+setting <tt>-diag</tt> to <tt>none</tt>.<p>
+If the color coding and legend labels of both matrices are identical,
+only one legend will be displayed, else two separate legends are
+displayed.<p>
+<tt>-title</tt> can be set to <tt>none</tt> to suppress the title, or to
+<tt>ylabel</tt> to show the title in the Y-label position (alongside
+the Y-axis).<p>
+With the <tt>-rainbow</tt> option dull grey-scale matrices can be turned
+into attractive color pictures.<p>
+Merged or rainbowed matrices can be written to an XPixelMap file with
+the <tt>-<a href="xpm.html">xpm</a></tt> option.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html"> root.xpm</a></tt> </TD><TD> Input </TD><TD> X PixMap compatible matrix file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f2</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html"> root2.xpm</a></tt> </TD><TD> Input, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-di</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="m2p.html"> ps.m2p</a></tt> </TD><TD> Input, Opt., Lib. </TD><TD> Input file for mat2ps </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-do</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="m2p.html"> out.m2p</a></tt> </TD><TD> Output, Opt. </TD><TD> Input file for mat2ps </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="eps.html"> plot.eps</a></tt> </TD><TD> Output, Opt. </TD><TD> Encapsulated PostScript (tm) file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-xpm</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html"> root.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]frame</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Display frame, ticks, labels, title and legend </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-title</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>top</tt> </TD><TD> Show title at: <a href="top.html">top</a>, ylabel or none </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-legend</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>both</tt> </TD><TD> Show legend: both, first, second or none </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-diag</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>first</tt> </TD><TD> Diagonal: first, second or none </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-bx</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Box x-size (also y-size when -by is not set) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-by</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Box y-size </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-rainbow</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>no</tt> </TD><TD> Rainbow colors, convert white to: no, blue or red </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-skip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> only write out every nr-th row and column </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]zeroline</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> insert line in <a href="xpm.html">xpm</a> matrix where axis label is zero </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<TITLE>xrama</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>xrama</H2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
+xrama shows a Ramachandran movie, that is, it shows
+the Phi/Psi angles as a function of time in an X-Window.<p>Static Phi/Psi plots for printing can be made with <a href="g_rama.html">g_rama</a>.<p>
+Some of the more common X command line options can be used:<br>
+-bg, -fg change colors, -font fontname, changes the font.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
<title>xtc file format</title>
-<body>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
<h2>xtc file format</h2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
The xtc format is a <b>portable</b> format for trajectories.
It uses the <i>xdr</i> routines for writing and reading
data which was created for the Unix NFS system. The trajectories
on your linker command line.
The source for this test can be found in file
<tt>$(GMXHOME)/src/gmxlib/testxtcf.f</ff>.
-
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
</body>
<title>xvgr</title>
-<body>
-<h1>XVGR, The ultimate plotting program</h1>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<h2>GRACE/XMGR, The ultimate plotting program</h2>
+<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
+<TR>
+<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
+<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
+<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<H3>Description</H3>
Almost all output from GROMACS analysis tools is ready as input for
-xvgr. We use xvgr, because it is very flexible, and it is also
+Grace, formerly known as Xmgr. We use Grace, because it is very flexible, and it is also
free software. It produces PostScript(tm) output, which is very suitable
for inclusion in eg. LaTeX documents, but also for other word processors.
<p>
-A sample xvgr session with GROMACS data is shown in this
-plot.<br>
+A sample Grace session with GROMACS data is shown below.<br><br>
<img src="../gif/xvgr.gif" alt="xvgr window"> <br>
<p>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
</body>
$(INSTALL_DATA) Template.mak $(DESTDIR)$(templatedir)/Makefile;
-CLEANFILES = *~ \\\#* *.ene *.hat *.tr? *.xtc *.edr *.ene *.xvg core *.log mdout.mdp *.tp? mon.out confout.gro deshuf.ndx output.* *.gz *.ps *.dat *.g87 *~ \\\#* Template.mak
+CLEANFILES = *~ \\\#* *.ene *.hat *.tr? *.xtc *.edr *.ene *.xvg core *.log mdout.mdp *.tp? mon.out confout.gro deshuf.ndx output.* *.gz *.ps *.dat *.g87 *~ \\\#*
cat << _EOF_
-----------------------------------------------------------------
-----------------------------------------------------------------
-This is the GROMACS demo. ( This demo takes about 15 to 30 min. )
+This is the GROMACS demo. ( This demo takes about 10-15 min. )
In this demo we will demonstrate you how to simulate Molecular
Dynamics (MD) using the GROMACS software package.
a pdb file of this peptide.
If you have a problem or remark with respect to this demonstration,
-please mail to: gromacs@chem.rug.nl
+please mail to: gromacs@gromacs.org , or check the resources on
+our website http://www.gromacs.org .
-----------------------------------------------------------------
-----------------------------------------------------------------
_EOF_
cat << _EOF_
-----------------------------------------------------------------
-----------------------------------------------------------------
-Before we you can actually start the GROMACS demo, I am going to check
-if GROMACS is installed properly on your system. If GROMACS is not
-installed properly on your computer, I strongly recommend you to
-contact your system manager.
+Before we you can actually start the GROMACS demo, the programs
+must be present in your PATH. This might already be the case if
+they are linked to /usr/local/bin. If not, follow the instructions
+in the getting started section. If GROMACS is not installed
+properly on your computer, contact your system manager.
-----------------------------------------------------------------
-----------------------------------------------------------------
_EOF_
_EOF_
if ( $?DISPLAY ) then
- echo "Because your DISPLAY variable is set, I will pop up a"
- echo "window with the output of the pdb2gmx program"
+ echo "You seem to have the DISPLAY variable is set, so we will"
+ echo "pop up a window with the output of the pdb2gmx program"
endif
echo -n "Press <enter>"
set ans = $<
_EOF_
if ( $?DISPLAY ) then
- echo "Because your DISPLAY variable is set, I will pop up a"
- echo "window with the output of the genbox program"
+ echo "The output of the genbox program should appear"
+ echo "in a separate xterm window!"
endif
echo -n "Press <enter>"
Before we can start the Energy Minimisation we have to preprocess all
the input files with the GROMACS preprocessor named grompp. grompp
preprocesses the topology file (.top), the structure file (.gro) and a
-parameter file (.mdp) resulting in a binary topology file (.tpb/.tpr
+parameter file (.mdp) resulting in a binary topology file (.tpr
extension). This binary topology file contains all information for a
simulation (in this case an energy minimisation).
-----------------------------------------------------------------
_EOF_
if ( $?DISPLAY ) then
- echo "Because your DISPLAY variable is set, I will pop up a"
- echo "window with the output of the grompp program"
+ echo "The output of the grompp program should appear"
+ echo "in a separate xterm window!"
endif
echo -n "Press <enter>"
define = -DFLEX_SPC
constraints = none
integrator = steep
-tinit = 0.0
dt = 0.002 ; ps !
nsteps = 100
nstlist = 10
ns_type = grid
-deltagrid = 2
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
_EOF_
if ( $?DISPLAY ) then
- echo "Because your DISPLAY variable is set, I will pop up a"
- echo "window with the output of the mdrun program"
+ echo "The output of the mdrun program should appear"
+ echo "in a separate xterm window!"
endif
echo -n "Press <enter>"
_EOF_
if ( $?DISPLAY ) then
- echo "Because your DISPLAY variable is set, I will pop up a"
- echo "window with the output of the grompp program"
+ echo "The output of the grompp program should appear"
+ echo "in a separate xterm window!"
endif
echo -n "Press <enter>"
title = ${MOL} position restraining
warnings = 10
cpp = /lib/cpp
-define = -DPOSRE
+define = -DPOSRES
constraints = all-bonds
integrator = md
-tinit = 0.0
dt = 0.002 ; ps !
nsteps = 500 ; total 1.0 ps.
nstcomm = 1
nstenergy = 10
nstlist = 10
ns_type = grid
-deltagrid = 2
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
-box = rectangular
-; Temperature coupling is on in two groups
-Tcoupl = yes
+; Berendsen temperature coupling is on in two groups
+Tcoupl = berendsen
tau_t = 0.1 0.1
tc-grps = protein sol
ref_t = 300 300
_EOF_
if ( $?DISPLAY ) then
- echo "Because your DISPLAY variable is set, I will pop up a"
- echo "window with the output of the grompp program"
+ echo "The output of the grompp program should appear"
+ echo "in a separate xterm window!"
endif
echo -n "Press <enter>"
cpp = /lib/cpp
constraints = all-bonds
integrator = md
-tinit = 0.0
dt = 0.002 ; ps !
nsteps = 5000 ; total 5 ps.
nstcomm = 1
nstfout = 0
nstlist = 10
ns_type = grid
-deltagrid = 2
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
-box = rectangular
-; Temperature coupling is on in two groups
-Tcoupl = yes
+; Berendsen temperature coupling is on in two groups
+Tcoupl = berendsen
tau_t = 0.1 0.1
tc-grps = protein sol
ref_t = 300 300
_EOF_
if ( $?DISPLAY ) then
- echo "Because your DISPLAY variable is set, I will pop up a"
- echo "window with the output of the mdrun program"
+ echo "The output of the mdrun program should appear"
+ echo "in a separate xterm window!"
endif
echo -n "Press <enter>"
ngmx -f ${MOL}_md -s ${MOL}_md &
endif
#last line
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
nsteps = 5000
; number of steps for center of mass motion removal =
nstcomm = 1
+comm-grps =
; LANGEVIN DYNAMICS OPTIONS =
; Temperature, friction coefficient (amu/ps) and random seed =
-ld-temp = 300
-ld-fric = 0
+bd-temp = 300
+bd-fric = 0
ld-seed = 1993
; ENERGY MINIMIZATION OPTIONS =
nstlist = 100
; ns algorithm (simple or grid) =
ns_type = simple
-deltagrid = 2
-; Box type, rectangular, triclinic, none =
-box = Rectangular
+; Periodic boundary conditions: xyz or none =
+pbc = xyz
; nblist cut-off =
rlist = 1
domain-decomposition = no
rvdw-switch = 0
rvdw = 1
; Apply long range dispersion corrections for Energy and Pressure =
-bDispCorr = no
+DispCorr = no
; Spacing for the PME/PPPM FFT grid =
fourierspacing = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used =
; EWALD/PME/PPPM parameters =
pme_order = 4
ewald_rtol = 1e-05
+epsilon_surface = 0
optimize_fft = no
; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling =
-tcoupl = yes
+tcoupl = berendsen
; Groups to couple separately =
tc-grps = System
; Time constant (ps) and reference temperature (K) =
ref_t = 300
; Pressure coupling =
Pcoupl = no
+Pcoupltype = Isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p = 1
compressibility =
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs-warnangle = 30
-; Output frequency of the Lincs accuracy =
-nstLincsout = 1000
; Convert harmonic bonds to morse potentials =
morse = no
free-energy = no
init-lambda = 0
delta-lambda = 0
+sc-alpha = 0
+sc-sigma = 0.3
; Non-equilibrium MD stuff =
acc-grps =
accelerate =
freezegrps =
freezedim =
+cos-acceleration = 0
+energygrp_excl =
; Electric fields =
; Format is number of terms (int) and for all terms an amplitude (real) =
; User defined thingies =
user1-grps =
user2-grps =
-user3-grps =
userint1 = 0
userint2 = 0
userint3 = 0
+;
+; File 'mdout.mdp' was generated
+; By user: erik (214)
+; On host: gaugain.theophys.kth.se
+; At date: Tue May 15 20:00:22 2001
+;
; VARIOUS PREPROCESSING OPTIONS =
title = Yo
nsteps = 5000
; number of steps for center of mass motion removal =
nstcomm = 1
+comm-grps =
; LANGEVIN DYNAMICS OPTIONS =
; Temperature, friction coefficient (amu/ps) and random seed =
-ld-temp = 300
-ld-fric = 0
+bd-temp = 300
+bd-fric = 0
ld-seed = 1993
; ENERGY MINIMIZATION OPTIONS =
nstlist = 100
; ns algorithm (simple or grid) =
ns_type = simple
-deltagrid = 2
-; Box type, rectangular, triclinic, none =
-box = Rectangular
+; Periodic boundary conditions: xyz or none =
+pbc = xyz
; nblist cut-off =
rlist = 1
domain-decomposition = no
rvdw-switch = 0
rvdw = 1
; Apply long range dispersion corrections for Energy and Pressure =
-bDispCorr = no
+DispCorr = no
; Spacing for the PME/PPPM FFT grid =
fourierspacing = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used =
; EWALD/PME/PPPM parameters =
pme_order = 4
ewald_rtol = 1e-05
+epsilon_surface = 0
optimize_fft = no
; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling =
-tcoupl = yes
+tcoupl = berendsen
; Groups to couple separately =
tc-grps = System
; Time constant (ps) and reference temperature (K) =
ref_t = 300
; Pressure coupling =
Pcoupl = no
+Pcoupltype = Isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p = 1
compressibility =
gen_temp = 300.0
gen_seed = 173529
-; OPTIMIZATIONS FOR SOLVENT MODELS =
-; Solvent molecule name (blank: no optimization) =
-solvent-optimization =
-
; OPTIONS FOR BONDS =
constraints = none
; Type of constraint algorithm =
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs-warnangle = 30
-; Output frequency of the Lincs accuracy =
-nstLincsout = 1000
; Convert harmonic bonds to morse potentials =
morse = no
free-energy = no
init-lambda = 0
delta-lambda = 0
+sc-alpha = 0
+sc-sigma = 0.3
; Non-equilibrium MD stuff =
acc-grps =
accelerate =
freezegrps =
freezedim =
+cos-acceleration = 0
+energygrp_excl =
; Electric fields =
; Format is number of terms (int) and for all terms an amplitude (real) =
; User defined thingies =
user1-grps =
user2-grps =
-user3-grps =
userint1 = 0
userint2 = 0
userint3 = 0
nstcomm = 1
ns_type = grid
-deltagrid = 2
rlist = 1
rcoulomb = 1.0
rvdw = 1.0
cpp = /lib/cpp
constraints = all-bonds
integrator = md
-tinit = 0.0
dt = 0.002 ; ps !
nsteps = 5000 ; total 10 ps.
nstcomm = 1
nstenergy = 100
nstlist = 10
ns_type = grid
-deltagrid = 2
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
-; Temperature coupling is on in two groups
-Tcoupl = yes
+; Berendsen temperature coupling is on in two groups
+Tcoupl = berendsen
tc-grps = Protein SOL
tau_t = 0.1 0.1
ref_t = 300 300
; Energy monitoring
energygrps = Protein SOL
-; Pressure coupling is now on
-Pcoupl = isotropic
+; Isotropic pressure coupling is now on
+Pcoupl = berendsen
+Pcoupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
define = -DPOSRES
constraints = all-bonds
integrator = md
-tinit = 0.0
dt = 0.002 ; ps !
nsteps = 5000 ; total 10 ps.
nstcomm = 1
nstenergy = 10
nstlist = 10
ns_type = grid
-deltagrid = 2
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
-; Temperature coupling is on in two groups
-Tcoupl = yes
+; Berendsen temperature coupling is on in two groups
+Tcoupl = berendsen
tc-grps = Protein SOL
tau_t = 0.1 0.1
ref_t = 300 300
rlist = 0.85 ; cut-off for ns
rvdw = 0.85 ; cut-off for vdw
rcoulomb = 0.85 ; cut-off for coulomb
-Tcoupl = yes ; temperature bath (yes,no)
+Tcoupl = berendsen ; temperature coupling
ref_t = 300
tc-grps = System
tau_t = 0.1
-Pcoupl = isotropic ; pressure bath
+Pcoupl = berendsen ; pressure bath
+Pcoupltype = isotropic ; pressure geometry
tau_p = 0.5 ; p-coupoling time
compressibility = 4.5e-5
ref_p = 1.0
gen_vel = yes ; generate initial velocities
gen_temp = 300 ; initial temperature
gen_seed = 1993 ; random seed
+
+
+
+
+
+
#!/bin/csh -f
-#
-# This script creates the html manual pages in
-# the html subdirectory below the current working
-# directory.
-#
-
-echo "Generating html manual for GROMACS programs"
-echo "-------------------------------------------"
-
-if ( $#argv < 1 ) then
- echo "Error: provide the binary directory as first argument."
+if ( $#argv < 2 ) then
+ echo "Error: provide the binary directory as first argument,"
+ echo "and the location of programs.txt as the second."
exit
endif
-set GMXBINDIR = $1
+set GMXBINDIR = $1
+set PROGFILE = $2
+
+set dir = $cwd
+
+set VER = 3.0
+set MANDIR = online
+set HTML = $cwd/html
+set HTMLOL = $HTML/$MANDIR
+set HTMLIDX = $HTML/$MANDIR.html
+
+set GENERAL = "getting_started:Getting_Started flow:Flow_Chart files:File_Formats mdp_opt:mdp_options"
+
+cd $GMXBINDIR
+set PROGRAMS = [a-z]*
+cd $dir
-set dir = $cwd
+echo ""
+echo "Generating table of contents in $HTMLIDX"
+echo "-------------------------------------------"
-setenv VER 3.0
-setenv HTML $cwd/html
if ( ! -d $HTML ) mkdir $HTML
-setenv MANDIR online
-setenv HTMLOL $HTML/$MANDIR
if ( ! -d $HTMLOL ) mkdir $HTMLOL
-setenv INDEX $HTML/$MANDIR.html
-if ( -f $INDEX ) \rm $INDEX
-cat > $INDEX << EOD
+if ( -f $HTMLIDX ) \rm $HTMLIDX
+touch $HTMLIDX
+
+cat > $HTMLIDX << EOD
<HTML>
-<TITLE>GROMACS $VER Manual </TITLE>
-<BODY text="#000000" bgcolor="#FFFFFF">
-<H1>GROMACS $VER manual</H1>
+<TITLE>GROMACS $VER Online Reference </TITLE>
+<LINK rel=stylesheet href="online/style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>GROMACS $VER Online Reference</H2>
+<HR>
+<P>
<TABLE BORDER=0 CELLSPACING=0 CELLPADDING=10>
<TR>
<TD VALIGN=top WIDTH="25%">
<h3>General</h3>
-<A HREF="changes$VER.html">New features</a>
-<br>
-<br><A HREF="$MANDIR/getting_started.html">Getting Started</a>
-<br>
-<br><A HREF="$MANDIR/flow.html" >Flow chart</a>
-<br>
-<br><A HREF="$MANDIR/files.html" >File formats</a>
+EOD
+foreach i ( $GENERAL )
+ set file = `echo $i | cut -d: -f1`
+ set desc = `echo $i | cut -d: -f2 | sed 's/_/ /g'`
+ echo "<A HREF="\""$MANDIR/"$file".html"\"">"$desc"</a>" >> $HTMLIDX
+ echo "<br><br>" >> $HTMLIDX
+end
+cat >> $HTMLIDX <<EOD
+<A HREF="gmxfaq.html">FAQ</a>
<br>
-<br><A HREF="$MANDIR/mdp_opt.html" >mdp options</a>
+<br><A HREF="http://www.gromacs.org">GROMACS homepage</A>
</TD>
-<TD VALIGN=top WIDTH="75%">
+<TD VALIGN=top WIDTH=75%>
<h3>Programs</h3>
<multicol cols=5>
-<A HREF="$MANDIR/options.html" >Options</a>
+<A HREF="$MANDIR/options.html">Options</a>
<br>
EOD
+foreach program ( $PROGRAMS )
+ echo "<br><a href="$MANDIR/$program.html">$program</a>" >> $HTMLIDX
+end
+cat >> $HTMLIDX << EOD
+</multicol>
+</TD>
+</TR>
+</TABLE>
+<HR>
+<h3>Programs by Topic</h3>
+<multicol cols=3>
+EOD
+awk -F '|' -v mandir=$MANDIR '{\
+ if (NF) {\
+ if ( $1 == "HEAD" ) {\
+ hnr++;\
+ printf("<A HREF=\"#HNR%d\">%s</A><br>\n",hnr,$2);\
+ }\
+ }\
+}' $PROGFILE >> $HTMLIDX
+echo "</multicol> " >> $HTMLIDX
+awk -F '|' -v mandir=$MANDIR '{\
+ if (NF) {\
+ if ( $1 == "HEAD" ) {\
+ hnr++;\
+ printf("\n<A NAME=\"HNR%d\">\n",hnr);\
+ printf("<TABLE CELLSPACING=1>\n<TR><TD> \n");\
+ printf("<TR><TD COLSPAN=2><b>%s</b>\n",$2);\
+ } else if ( $1 == "END" ) {\
+ printf("</TABLE>\n");\
+ } else {\
+ printf("<TR><TD><A HREF=\"%s/%s.html\">%s</A><TD>%s\n",mandir,$1,$1,$2);\
+ }\
+ }\
+}' $PROGFILE >> $HTMLIDX
+cat >> $HTMLIDX <<EOD
+<p>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</body>
+</html>
+EOD
+echo "Generating html manual for GROMACS programs"
+echo "-------------------------------------------"
-cd $GMXBINDIR
-set PROGRAMS = [a-z]*
cd $dir
foreach program ( $PROGRAMS )
echo -n "$program "
cd $HTMLOL
$GMXBINDIR/$program -quiet -man html >& /dev/null
- cat >> $INDEX << EOK
-<br><a href="$MANDIR/$program.html">$program</a>
-EOK
endif
endif
end
-cat >> $INDEX << EOM
-</multicol>
-</TD>
-</TR>
-</TABLE>
-</BODY>
-</HTML>
-EOM
-
-echo ""
-echo ""
-echo "New html pages in $HTML"
-echo "file:$INDEX"
-
#last line
set GMXBINDIR = $1
+set dir = $cwd
+
set VER = 3.0
set MANDIR = online
-set HTML = $GMXHOME/html
+set HTML = $cwd/html
set HTMLOL = $HTML/$MANDIR
set HTMLIDX = $HTML/$MANDIR.html
-set TEXDIR = $GMXHOME/doc
-if ( ! -d $TEXDIR ) set TEXDIR = .
+set TEXDIR = $cwd/doc
set TEXIDX = $TEXDIR/proglist.tex
set PROGFILE = programs.txt
set GENERAL = "getting_started:Getting_Started flow:Flow_Chart files:File_Formats mdp_opt:mdp_options"
-set olddir = `pwd`
-cd $GMXHOME/bin/$GMXCPU
-set PROGRAMS =
-foreach program ( `\ls -1 | grep -v "#"` )
- if ( ( $program != average ) && ( $program != luck ) && ( $program != my_dssp ) ) then
- set PROGRAMS = "$PROGRAMS $program"
- endif
-end
-cd $olddir
+cd $GMXBINDIR
+set PROGRAMS = [a-z]*
+cd $dir
echo "generating html page $HTMLIDX"
+if ( ! -d $HTML ) mkdir $HTML
if ( -f $HTMLIDX ) \rm $HTMLIDX
touch $HTMLIDX
-echo "<HTML>" >> $HTMLIDX
-echo "<TITLE>GROMACS $VER Manual </TITLE>" >> $HTMLIDX
-echo "<BODY>" >> $HTMLIDX
-echo "<H1>GROMACS $VER manual</H1>" >> $HTMLIDX
-echo "<IMG SRC="\""gif/rainbow.gif"\"" WIDTH=100% HEIGHT=7>" >> $HTMLIDX
-echo "<P>" >> $HTMLIDX
-echo "<TABLE BORDER=0 CELLSPACING=0 CELLPADDING=10>" >> $HTMLIDX
-echo "<TR>" >> $HTMLIDX
-echo "<TD VALIGN=top WIDTH=25%>" >> $HTMLIDX
-echo "<h3>General</h3>" >> $HTMLIDX
+if ( ! -d $TEXDIR ) mkdir $TEXDIR
+
+cat > $HTMLIDX << EOD
+<HTML>
+<TITLE>GROMACS $VER Online Reference </TITLE>
+<LINK rel=stylesheet href="online/style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
+<H2>GROMACS $VER Online Reference</H2>
+<HR>
+<P>
+<TABLE BORDER=0 CELLSPACING=0 CELLPADDING=10>
+<TR>
+<TD VALIGN=top WIDTH="25%">
+<h3>General</h3>
+EOD
foreach i ( $GENERAL )
set file = `echo $i | cut -d: -f1`
set desc = `echo $i | cut -d: -f2 | sed 's/_/ /g'`
echo "<A HREF="\""$MANDIR/"$file".html"\"">"$desc"</a>" >> $HTMLIDX
echo "<br><br>" >> $HTMLIDX
end
-echo "<A HREF="\""gmxfaq.html"\"">FAQ</a>" >> $HTMLIDX
-echo "</TD>" >> $HTMLIDX
-echo "<TD VALIGN=top WIDTH=75%>" >> $HTMLIDX
-echo "<h3>Programs</h3>" >> $HTMLIDX
-echo "<multicol cols=5> " >> $HTMLIDX
-echo "<A HREF="\""$MANDIR/options.html"\"">Options</a>" >> $HTMLIDX
-echo "<br>" >> $HTMLIDX
+cat >> $HTMLIDX <<EOD
+<A HREF="gmxfaq.html">FAQ</a>
+<br>
+<br><A HREF="http://www.gromacs.org">GROMACS homepage</A>
+</TD>
+<TD VALIGN=top WIDTH=75%>
+<h3>Programs</h3>
+<multicol cols=5>
+<A HREF="$MANDIR/options.html">Options</a>
+<br>
+EOD
foreach program ( $PROGRAMS )
- echo "<br><a href="\""$MANDIR/$program.html"\"">$program</a>" >> $HTMLIDX
+ echo "<br><a href="$MANDIR/$program.html">$program</a>" >> $HTMLIDX
end
-echo "</multicol>" >> $HTMLIDX
-echo "</TD>" >> $HTMLIDX
-echo "</TR>" >> $HTMLIDX
-echo "</TABLE>" >> $HTMLIDX
-echo "<IMG SRC="\""gif/rainbow.gif"\"" WIDTH=100% HEIGHT=7>" >> $HTMLIDX
-echo "<h3>Programs by Topic</h3>" >> $HTMLIDX
-echo "<multicol cols=3> " >> $HTMLIDX
+cat >> $HTMLIDX << EOD
+</multicol>
+</TD>
+</TR>
+</TABLE>
+<HR>
+<h3>Programs by Topic</h3>
+<multicol cols=3>
+EOD
awk -F '|' -v mandir=$MANDIR '{\
if (NF) {\
if ( $1 == "HEAD" ) {\
}\
}\
}' $PROGFILE >> $HTMLIDX
-echo "<p>" >> $HTMLIDX
-echo "<IMG SRC="\""gif/rainbow.gif"\"" WIDTH=100% HEIGHT=7>" >> $HTMLIDX
-echo "<p>" >> $HTMLIDX
-echo "</BODY>" >> $HTMLIDX
-echo "</HTML>" >> $HTMLIDX
+cat >> $HTMLIDX <<EOD
+<p>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</body>
+</html>
+EOD
echo "generating latex page $TEXIDX"
--- /dev/null
+#!/bin/csh -f
+
+if ( $#argv < 2 ) then
+ echo "Error: provide the binary directory as first argument,"
+ echo "and the location of programs.txt as the second."
+ exit
+endif
+
+set GMXBINDIR = $1
+set PROGFILE = $2
+
+set dir = $cwd
+
+set VER = 3.0
+set TEXDIR = $cwd/doc
+set TEXIDX = $TEXDIR/proglist.tex
+set PROGFILE = programs.txt
+
+set GENERAL = "getting_started:Getting_Started flow:Flow_Chart files:File_Formats mdp_opt:mdp_options"
+
+cd $GMXBINDIR
+set PROGRAMS = [a-z]*
+cd $dir
+
+echo ""
+echo "generating latex page $TEXIDX"
+echo "--------------------------------"
+
+if ( ! -d $TEXDIR ) mkdir $TEXDIR
+
+if ( -f $TEXIDX ) \rm $TEXIDX
+touch $TEXIDX
+
+echo "\\begin{description}" >> $TEXIDX
+awk -F '|' -v mandir=$MANDIR -v longest="mk\\_angndx" '{\
+ gsub("_","\\_",$0);\
+ gsub("%","\\%",$0);\
+ if (NF) {\
+ if ( $1 == "LONGEST" ) {\
+ longest = $2;\
+ } else if ( $1 == "HEAD" ) {\
+ printf("\\item {\\large\\bf %s}\n",$2);\
+ printf("\\vspace{-2ex}\\begin{tabbing}\n");\
+ printf("{\\bf %s} \\= \\kill\n",longest);\
+ } else if ( $1 == "END" ) {\
+ printf("\\end{tabbing}\\vspace{-2ex}\n\n");\
+ } else {\
+ printf("{\\bf %s} \\> %s \\\\\n",$1,$2);\
+ }\
+ }\
+}' $PROGFILE | sed -e 's/e\.g\./{\\eg}/g' >> $TEXIDX
+echo "\end{description}" >> $TEXIDX
+
+#last line
#define NSR(s) check_html(s,program)
fprintf(out,"<TITLE>%s</TITLE>\n",program);
- fprintf(out,"<LINK rel=stylesheet href=\"style.css\" type=\"text/css\">");
- fprintf(out,"<BODY text=\"#000000\" bgcolor=\"#FFFFFF\" link=\"#0000EF\" vlink=\"#006500\" alink=\"#FF0000\">\n");
+ fprintf(out,"<LINK rel=stylesheet href=\"style.css\" type=\"text/css\">\n");
+ fprintf(out,"<BODY text=\"#000000\" bgcolor=\"#FFFFFF\" link=\"#0000EF\" vlink=\"#650065\" alink=\"#FF0000\">\n");
fprintf(out,"<H2>%s</H2>\n",program);
- fprintf(out,"<B>%s</B><BR>\n<B>%s</B><P>",GromacsVersion(),mydate());
+ fprintf(out,"<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH=\"98%\">\n");
+ fprintf(out,"<TR>\n<TD><font size=-1><A HREF=\"../online.html\">Main Table of Contents</A></font></TD>\n");
+ fprintf(out,"<TD ALIGN=RIGHT><B>%s</B></TR>\n",GromacsVersion());
+ fprintf(out,"<TR><TD><font size=-1><A HREF=\"http://www.gromacs.org\">GROMACS homepage</A></font></TD>\n");
+ fprintf(out,"<TD ALIGN=RIGHT><B>%s</B></TR></TABLE></CENTER><HR>\n",mydate());
if (nldesc > 0) {
fprintf(out,"<H3>Description</H3>\n");
fprintf(out,"</UL>\n");
}
fprintf(out,"<P>\n");
+ fprintf(out,"<hr>\n<div ALIGN=RIGHT>\n");
+ fprintf(out,"<font size=\"-1\"><a href=\"http://www.gromacs.org\">"
+ "http://www.gromacs.org</a></font><br>\n");
+ fprintf(out,"<font size=\"-1\"><a href=\"mailto:gromacs@gromacs.org\">"
+ "gromacs@gromacs.org</a></font><br>\n");
+ fprintf(out,"</div>\n");
fprintf(out,"</BODY>\n");
}
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff
