+++ /dev/null
-.TH anadock_d 1 "Thu 16 Oct 2008"
-.SH NAME
-anadock_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3anadock_d\fP
-.BI "-f" " eiwit.pdb "
-.BI "-ox" " cluster.pdb "
-.BI "-od" " edocked.xvg "
-.BI "-of" " efree.xvg "
-.BI "-g" " anadock.log "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-[no]xvgr" ""
-.BI "-[no]free" ""
-.BI "-[no]rms" ""
-.BI "-cutoff" " real "
-.SH DESCRIPTION
-anadock analyses the results of an Autodock run and clusters the
-structures together, based on distance or RMSD. The docked energy
-and free energy estimates are analysed, and for each cluster the
-energy statistics are printed.
-
-
-An alternative approach to this is to cluster the structures first
-(using
-.B g_cluster
-and then sort the clusters on either lowest
-energy or average energy.
-.SH FILES
-.BI "-f" " eiwit.pdb"
-.B Input
- Protein data bank file
-
-.BI "-ox" " cluster.pdb"
-.B Output
- Protein data bank file
-
-.BI "-od" " edocked.xvg"
-.B Output
- xvgr/xmgr file
-
-.BI "-of" " efree.xvg"
-.B Output
- xvgr/xmgr file
-
-.BI "-g" " anadock.log"
-.B Output
- Log file
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 0"
- Set the nicelevel
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.BI "-[no]free" "no "
- Use Free energy estimate from autodock for sorting the classes
-
-.BI "-[no]rms" "yes "
- Cluster on RMS or distance
-
-.BI "-cutoff" " real" " 0.2 "
- Maximum RMSD/distance for belonging to the same cluster
-
+++ /dev/null
-.TH do_dssp_d 1 "Thu 16 Oct 2008"
-.SH NAME
-do_dssp_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3do_dssp_d\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 "-nice" " int "
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-dt" " time "
-.BI "-tu" " enum "
-.BI "-[no]w" ""
-.BI "-[no]xvgr" ""
-.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
-/usr/local/bin/dssp. If this is not the case, then you should
-set an environment variable
-.B DSSP
-pointing to the dssp
-executable, e.g.:
-
-
-
-.B setenv DSSP /opt/dssp/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
-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 xml
-
-.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 "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- Only use frame when t MOD dt = first time (ps)
-
-.BI "-tu" " enum" " ps"
- Time unit:
-.B ps
-,
-.B fs
-,
-.B ns
-,
-.B us
-,
-.B ms
-or
-.B s
-
-
-.BI "-[no]w" "no "
- View output xvg, xpm, eps and pdb files
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.BI "-sss" " string" " HEBT"
- Secondary structures for structure count
-
+++ /dev/null
-.TH editconf_d 1 "Thu 16 Oct 2008"
-.SH NAME
-editconf_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3editconf_d\fP
-.BI "-f" " conf.gro "
-.BI "-n" " index.ndx "
-.BI "-o" " out.gro "
-.BI "-mead" " mead.pqr "
-.BI "-bf" " bfact.dat "
-.BI "-[no]h" ""
-.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 "-translate" " vector "
-.BI "-rotate" " vector "
-.BI "-[no]princ" ""
-.BI "-scale" " vector "
-.BI "-density" " real "
-.BI "-[no]vol" ""
-.BI "-[no]pbc" ""
-.BI "-[no]grasp" ""
-.BI "-rvdw" " real "
-.BI "-sig56" " real "
-.BI "-[no]vdwread" ""
-.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 triclinic
-is a
-triclinic box,
-.B cubic
-is a rectangular box with all sides equal
-
-.B dodecahedron
-represents 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 a
-.B triclinic
-box 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
-boxes, the dimensions are set
-to the diameter of the system (largest distance between atoms) plus twice
-the specified distance.
-
-
-
-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.
-
-
-
-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 (pqr) 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.
-
-
-To convert a truncated octrahedron file produced by a package which uses
-a cubic box with the corners cut off (such as Gromos) use:
-
-
-.B editconf -f in -rotate 0 45 35.264 -bt o -box veclen -o out
-
-
-where
-.B veclen
-is the size of the cubic box times sqrt(3)/2.
-.SH FILES
-.BI "-f" " conf.gro"
-.B Input
- Generic structure: gro g96 pdb tpr tpb tpa xml
-
-.BI "-n" " index.ndx"
-.B Input, Opt.
- Index file
-
-.BI "-o" " out.gro"
-.B Output, Opt.
- Generic structure: gro g96 pdb xml
-
-.BI "-mead" " mead.pqr"
-.B Output, Opt.
- Coordinate file for MEAD
-
-.BI "-bf" " bfact.dat"
-.B Input, Opt.
- Generic data file
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.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" " triclinic"
- Box type for -box and -d:
-.B triclinic
-,
-.B cubic
-,
-.B dodecahedron
-or
-.B 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 "-translate" " vector" " 0 0 0"
- Translation
-
-.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]vol" "yes "
- Compute and print volume of the box
-
-.BI "-[no]pbc" "no "
- Remove the periodicity (make molecule whole again)
-
-.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 (in nm) if one can not be found in the database or if no parameters are present in the topology file
-
-.BI "-sig56" " real" " 0 "
- Use rmin/2 (minimum in the Van der Waals potential) rather than sigma/2
-
-.BI "-[no]vdwread" "no "
- Read the Van der Waals radii from the file vdwradii.dat rather than computing the radii based on the force field
-
-.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 KNOWN PROBLEMS
-\- For complex molecules, the periodicity removal routine may break down, in that case you can use trjconv
-
+++ /dev/null
-.TH eneconv_d 1 "Thu 16 Oct 2008"
-.SH NAME
-eneconv_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3eneconv_d\fP
-.BI "-f" " ener.edr "
-.BI "-o" " fixed.edr "
-.BI "-[no]h" ""
-.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
-With
-.I multiple files
-specified for the
-.B -f
-option:
-
-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
-.I one file
-specified for
-.B -f
-:
-
-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, Mult.
- Generic energy: edr ene
-
-.BI "-o" " fixed.edr"
-.B Output
- Generic energy: edr ene
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.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 KNOWN PROBLEMS
-\- 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_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_anaeig_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_anaeig_d\fP
-.BI "-v" " eigenvec.trr "
-.BI "-v2" " eigenvec2.trr "
-.BI "-f" " traj.xtc "
-.BI "-s" " topol.tpr "
-.BI "-n" " index.ndx "
-.BI "-eig" " eigenval.xvg "
-.BI "-eig2" " eigenval2.xvg "
-.BI "-comp" " eigcomp.xvg "
-.BI "-rmsf" " eigrmsf.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 "-nice" " int "
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-dt" " time "
-.BI "-tu" " enum "
-.BI "-[no]w" ""
-.BI "-[no]xvgr" ""
-.BI "-first" " int "
-.BI "-last" " int "
-.BI "-skip" " int "
-.BI "-max" " real "
-.BI "-nframes" " int "
-.BI "-[no]split" ""
-.BI "-[no]entropy" ""
-.BI "-temp" " real "
-.BI "-nevskip" " int "
-.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 -comp
-: plot the vector components per atom of eigenvectors
-
-.B -first
-to
-.B -last
-.
-
-
-
-.B -rmsf
-: plot the RMS fluctuation per atom of eigenvectors
-
-.B -first
-to
-.B -last
-(requires
-.B -eig
-).
-
-
-
-.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 -eig
-,
-.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.
-
-
-When the
-.B -entropy
-flag is given an entropy estimate will be
-computed based on the Quasiharmonic approach and based on
-Schlitter's formula.
-.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 xml
-
-.BI "-n" " index.ndx"
-.B Input, Opt.
- Index file
-
-.BI "-eig" " eigenval.xvg"
-.B Input, Opt.
- xvgr/xmgr file
-
-.BI "-eig2" " eigenval2.xvg"
-.B Input, Opt.
- xvgr/xmgr file
-
-.BI "-comp" " eigcomp.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.BI "-rmsf" " eigrmsf.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 xml
-
-.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 "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- Only use frame when t MOD dt = first time (ps)
-
-.BI "-tu" " enum" " ps"
- Time unit:
-.B ps
-,
-.B fs
-,
-.B ns
-,
-.B us
-,
-.B ms
-or
-.B s
-
-
-.BI "-[no]w" "no "
- View output xvg, xpm, eps and pdb files
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.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
-
-.BI "-[no]entropy" "no "
- Compute entropy according to the Quasiharmonic formula or Schlitter's method.
-
-.BI "-temp" " real" " 298.15"
- Temperature for entropy calculations
-
-.BI "-nevskip" " int" " 6"
- Number of eigenvalues to skip when computing the entropy due to the quasi harmonic approximation. When you do a rotational and/or translational fit prior to the covariance analysis, you get 3 or 6 eigenvalues that are very close to zero, and which should not be taken into account when computing the entropy.
-
+++ /dev/null
-.TH g_analyze_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_analyze_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_analyze_d\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 "-g" " fitlog.log "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-[no]w" ""
-.BI "-[no]xvgr" ""
-.BI "-[no]time" ""
-.BI "-b" " real "
-.BI "-e" " real "
-.BI "-n" " int "
-.BI "-[no]d" ""
-.BI "-bw" " real "
-.BI "-errbar" " enum "
-.BI "-[no]integrate" ""
-.BI "-aver_start" " real "
-.BI "-[no]xydy" ""
-.BI "-[no]regression" ""
-.BI "-[no]luzar" ""
-.BI "-temp" " real "
-.BI "-fitstart" " real "
-.BI "-smooth" " real "
-.BI "-filter" " real "
-.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(i pi t) 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 is:
-
-f(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 f2(t) to error2.
-When the actual block average is very close to the analytical curve,
-the error is sigma*sqrt(2/T (a tau1 + (1-a) tau2)).
-The complete derivation is given in
-B. Hess, J. Chem. Phys. 116:209-217, 2002.
-
-
-Option
-.B -filter
-prints the RMS high-frequency fluctuation
-of each set and over all sets with respect to a filtered average.
-The filter is proportional to cos(pi t/len) where t goes from -len/2
-to len/2. len is supplied with the option
-.B -filter
-.
-This filter reduces oscillations with period len/2 and len by a factor
-of 0.79 and 0.33 respectively.
-
-
-Option
-.B -g
-fits the data to the function given with option
-
-.B -fitfn
-.
-
-
-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.
-
-Option
-.B -luzar
-performs a Luzar & Chandler kinetics analysis
-on output from
-.B g_hbond
-.B . The input file can be taken directly
-from
-.B g_hbond -ac
-, and then the same result should be produced.
-.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
-
-.BI "-g" " fitlog.log"
-.B Output, Opt.
- Log file
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 0"
- Set the nicelevel
-
-.BI "-[no]w" "no "
- View output xvg, xpm, eps and pdb files
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.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:
-.B none
-,
-.B stddev
-,
-.B error
-or
-.B 90
-
-
-.BI "-[no]integrate" "no "
- Integrate data function(s) numerically using trapezium rule
-
-.BI "-aver_start" " real" " 0 "
- Start averaging the integral from here
-
-.BI "-[no]xydy" "no "
- Interpret second data set as error in the y values for integrating
-
-.BI "-[no]regression" "no "
- Perform a linear regression analysis on the data
-
-.BI "-[no]luzar" "no "
- Do a Luzar and Chandler analysis on a correlation function and related as produced by g_hbond. When in addition the -xydy flag is given the second and fourth column will be interpreted as errors in c(t) and n(t).
-
-.BI "-temp" " real" " 298.15"
- Temperature for the Luzar hydrogen bonding kinetics analysis
-
-.BI "-fitstart" " real" " 1 "
- Time (ps) from which to start fitting the correlation functions in order to obtain the forward and backward rate constants for HB breaking and formation
-
-.BI "-smooth" " real" " -1 "
- If = 0, the tail of the ACF will be smoothed by fitting it to an exponential function: y = A exp(-x/tau)
-
-.BI "-filter" " real" " 0 "
- Print the high-frequency fluctuation after filtering with a cosine filter of length
-
-.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):
-.B 0
-,
-.B 1
-,
-.B 2
-or
-.B 3
-
-
-.BI "-fitfn" " enum" " none"
- Fit function:
-.B none
-,
-.B exp
-,
-.B aexp
-,
-.B exp_exp
-,
-.B vac
-,
-.B exp5
-,
-.B exp7
-or
-.B exp9
-
-
-.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_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_angle_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_angle_d\fP
-.BI "-f" " traj.xtc "
-.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 "-or" " traj.trr "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-dt" " time "
-.BI "-[no]w" ""
-.BI "-[no]xvgr" ""
-.BI "-type" " enum "
-.BI "-[no]all" ""
-.BI "-binwidth" " real "
-.BI "-[no]periodic" ""
-.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.
-
-
-With option
-.B -or
-a trajectory file is dumped containing cos andsin of selected dihedral angles which subsequently can be used as
-input for a PCA analysis using
-.B g_covar
-.
-.SH FILES
-.BI "-f" " traj.xtc"
-.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
-
-.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
-
-.BI "-or" " traj.trr"
-.B Output, Opt.
- Trajectory in portable xdr format
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- Only use frame when t MOD dt = first time (ps)
-
-.BI "-[no]w" "no "
- View output xvg, xpm, eps and pdb files
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.BI "-type" " enum" " angle"
- Type of angle to analyse:
-.B angle
-,
-.B dihedral
-,
-.B improper
-or
-.B 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]periodic" "yes "
- Print dihedral angles modulo 360 degrees
-
-.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):
-.B 0
-,
-.B 1
-,
-.B 2
-or
-.B 3
-
-
-.BI "-fitfn" " enum" " none"
- Fit function:
-.B none
-,
-.B exp
-,
-.B aexp
-,
-.B exp_exp
-,
-.B vac
-,
-.B exp5
-,
-.B exp7
-or
-.B exp9
-
-
-.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 KNOWN PROBLEMS
-\- Counting transitions only works for dihedrals with multiplicity 3
-
+++ /dev/null
-.TH g_bond_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_bond_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_bond_d\fP
-.BI "-f" " traj.xtc "
-.BI "-n" " index.ndx "
-.BI "-s" " topol.tpr "
-.BI "-o" " bonds.xvg "
-.BI "-l" " bonds.log "
-.BI "-d" " distance.xvg "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-dt" " time "
-.BI "-[no]w" ""
-.BI "-[no]xvgr" ""
-.BI "-blen" " real "
-.BI "-tol" " real "
-.BI "-[no]aver" ""
-.BI "-[no]averdist" ""
-.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.
-
-
-Option
-.B -d
-plots all the distances as a function of time.
-This requires a structure file for the atom and residue names in
-the output. If however the option
-.B -averdist
-is given (as well
-or separately) the average bond length is plotted instead.
-.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, Opt.
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
-
-.BI "-o" " bonds.xvg"
-.B Output
- xvgr/xmgr file
-
-.BI "-l" " bonds.log"
-.B Output, Opt.
- Log file
-
-.BI "-d" " distance.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- Only use frame when t MOD dt = first time (ps)
-
-.BI "-[no]w" "no "
- View output xvg, xpm, eps and pdb files
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.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 "
- Average bond length distributions
-
-.BI "-[no]averdist" "yes "
- Average distances (turns on -d)
-
-.SH KNOWN PROBLEMS
-\- It should be possible to get bond information from the topology.
-
+++ /dev/null
-.TH g_bundle_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_bundle_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_bundle_d\fP
-.BI "-f" " traj.xtc "
-.BI "-s" " topol.tpr "
-.BI "-n" " index.ndx "
-.BI "-ol" " bun_len.xvg "
-.BI "-od" " bun_dist.xvg "
-.BI "-oz" " bun_z.xvg "
-.BI "-ot" " bun_tilt.xvg "
-.BI "-otr" " bun_tiltr.xvg "
-.BI "-otl" " bun_tiltl.xvg "
-.BI "-ok" " bun_kink.xvg "
-.BI "-okr" " bun_kinkr.xvg "
-.BI "-okl" " bun_kinkl.xvg "
-.BI "-oa" " axes.pdb "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-dt" " time "
-.BI "-tu" " enum "
-.BI "-[no]xvgr" ""
-.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 centers of mass of these parts
-define the tops and bottoms of the axes.
-Several quantities are written to file:
-the axis length, the distance and the z-shift of the axis mid-points
-with respect to the average center of all axes, the total tilt,
-the radial tilt and the lateral tilt with respect to the average axis.
-
-
-
-With options
-.B -ok
-,
-.B -okr
-and
-.B -okl
-the total,
-radial and lateral kinks of the axes are plotted. An extra index
-group of kink atoms is required, which is also divided into
-.B -na
-
-parts. The kink angle is defined as the angle between the kink-top and
-the bottom-kink vectors.
-
-
-
-With option
-.B -oa
-the top, mid (or kink when
-.B -ok
-is set)
-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 xml
-
-.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 "-oz" " bun_z.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 "-ok" " bun_kink.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.BI "-okr" " bun_kinkr.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.BI "-okl" " bun_kinkl.xvg"
-.B Output, Opt.
- 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 "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- Only use frame when t MOD dt = first time (ps)
-
-.BI "-tu" " enum" " ps"
- Time unit:
-.B ps
-,
-.B fs
-,
-.B ns
-,
-.B us
-,
-.B ms
-or
-.B s
-
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.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_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_chi_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_chi_d\fP
-.BI "-s" " 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 "-ot" " dihtrans.xvg "
-.BI "-oh" " trhisto.xvg "
-.BI "-rt" " restrans.xvg "
-.BI "-cp" " chiprodhisto.xvg "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-dt" " time "
-.BI "-[no]w" ""
-.BI "-[no]xvgr" ""
-.BI "-r0" " int "
-.BI "-[no]phi" ""
-.BI "-[no]psi" ""
-.BI "-[no]omega" ""
-.BI "-[no]rama" ""
-.BI "-[no]viol" ""
-.BI "-[no]periodic" ""
-.BI "-[no]all" ""
-.BI "-[no]rad" ""
-.BI "-[no]shift" ""
-.BI "-binwidth" " int "
-.BI "-core_rotamer" " real "
-.BI "-maxchi" " enum "
-.BI "-[no]normhisto" ""
-.BI "-[no]ramomega" ""
-.BI "-bfact" " real "
-.BI "-[no]chi_prod" ""
-.BI "-[no]HChi" ""
-.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.
-The distributions (histo-(dihedral)(RESIDUE).xvg) are cumulative over all residues of each type.
-
-
-If option
-.B -corr
-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).
-Separate files for each dihedral of each residue
-(corr(dihedral)(RESIDUE)(nresnr).xvg) are output, as well as a
-file containing the information for all residues (argument of
-.B -corr
-).
-
-
-With option
-.B -all
-, the angles themselves as a function of time for
-each residue are printed to separate files (dihedral)(RESIDUE)(nresnr).xvg.
-These can be in radians or degrees.
-
-
-A log file (argument
-.B -g
-) is also written. This contains
-
-(a) information about the number of residues of each type.
-
-(b) The NMR 3J coupling constants from the Karplus equation.
-
-(c) a table for each residue of the number of transitions between
-rotamers per nanosecond, and the order parameter S2 of each dihedral.
-
-(d) a table for each residue of the rotamer occupancy.
-
-All rotamers are taken as 3-fold, except for omegas and chi-dihedrals
-to planar groups (i.e. chi2 of aromatics asp and asn, chi3 of glu
-and gln, and chi4 of arg), which are 2-fold. "rotamer 0" means
-that the dihedral was not in the core region of each rotamer.
-The width of the core region can be set with
-.B -core_rotamer
-
-
-
-The S2 order parameters are also output to an xvg file
-(argument
-.B -o
-) and optionally as a pdb file with
-the S2 values as B-factor (argument
-.B -p
-).
-The total number of rotamer transitions per timestep
-(argument
-.B -ot
-), the number of transitions per rotamer
-(argument
-.B -rt
-), and the 3J couplings (argument
-.B -jc
-),
-can also be written to .xvg files.
-
-
-If
-.B -chi_prod
-is set (and maxchi 0), cumulative rotamers, e.g.
-1+9(chi1-1)+3(chi2-1)+(chi3-1) (if the residue has three 3-fold
-dihedrals and maxchi = 3)
-are calculated. As before, if any dihedral is not in the core region,
-the rotamer is taken to be 0. The occupancies of these cumulative
-rotamers (starting with rotamer 0) are written to the file
-that is the argument of
-.B -cp
-, and if the
-.B -all
-flag
-is given, the rotamers as functions of time
-are written to chiproduct(RESIDUE)(nresnr).xvg
-and their occupancies to histo-chiproduct(RESIDUE)(nresnr).xvg.
-
-
-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 "-s" " conf.gro"
-.B Input
- Generic structure: gro g96 pdb tpr tpb tpa xml
-
-.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
-
-.BI "-ot" " dihtrans.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.BI "-oh" " trhisto.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.BI "-rt" " restrans.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.BI "-cp" " chiprodhisto.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- Only use frame when t MOD dt = first time (ps)
-
-.BI "-[no]w" "no "
- View output xvg, xpm, eps and pdb files
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.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]periodic" "yes "
- Print dihedral angles modulo 360 degrees
-
-.BI "-[no]all" "no "
- Output separate files for every dihedral.
-
-.BI "-[no]rad" "no "
- in angle vs time files, use radians rather than degrees.
-
-.BI "-[no]shift" "no "
- Compute chemical shifts from Phi/Psi angles
-
-.BI "-binwidth" " int" " 1"
- bin width for histograms (degrees)
-
-.BI "-core_rotamer" " real" " 0.5 "
- only the central -core_rotamer*(360/multiplicity) belongs to each rotamer (the rest is assigned to rotamer 0)
-
-.BI "-maxchi" " enum" " 0"
- calculate first ndih Chi dihedrals:
-.B 0
-,
-.B 1
-,
-.B 2
-,
-.B 3
-,
-.B 4
-,
-.B 5
-or
-.B 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 "-[no]chi_prod" "no "
- compute a single cumulative rotamer for each residue
-
-.BI "-[no]HChi" "no "
- Include dihedrals to sidechain hydrogens
-
-.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):
-.B 0
-,
-.B 1
-,
-.B 2
-or
-.B 3
-
-
-.BI "-fitfn" " enum" " none"
- Fit function:
-.B none
-,
-.B exp
-,
-.B aexp
-,
-.B exp_exp
-,
-.B vac
-,
-.B exp5
-,
-.B exp7
-or
-.B exp9
-
-
-.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 KNOWN PROBLEMS
-\- 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.
-
-\- Phi and psi dihedrals are calculated in a non-standard way, using H-N-CA-C for phi instead of C(-)-N-CA-C, and N-CA-C-O for psi instead of N-CA-C-N(+). This causes (usually small) discrepancies with the output of other tools like g_rama.
-
-\- -r0 option does not work properly
-
-\- Rotamers with multiplicity 2 are printed in chi.log as if they had multiplicity 3, with the 3rd (g(+)) always having probability 0
-
+++ /dev/null
-.TH g_cluster_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_cluster_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_cluster_d\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 "-nice" " int "
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-dt" " time "
-.BI "-tu" " enum "
-.BI "-[no]w" ""
-.BI "-[no]xvgr" ""
-.BI "-[no]dista" ""
-.BI "-nlevels" " int "
-.BI "-cutoff" " real "
-.BI "-[no]fit" ""
-.BI "-max" " real "
-.BI "-skip" " int "
-.BI "-[no]av" ""
-.BI "-wcl" " int "
-.BI "-nst" " int "
-.BI "-rmsmin" " real "
-.BI "-method" " enum "
-.BI "-minstruct" " int "
-.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.
-
-
-single 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 (single 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.
-
-Two output files are always written:
-
-
-.B -o
-writes the RMSD values in the upper left half of the matrix
-and a graphical depiction of the clusters in the lower right half
-When
-.B -minstruct
-= 1 the graphical depiction is black
-when two structures are in the same cluster.
-When
-.B -minstruct
- 1 different colors will be used for each
-cluster.
-
-
-.B -g
-writes information on the options used and a detailed list
-of all clusters and their members.
-
-
-Additionally, a number of optional output files can be written:
-
-
-.B -dist
-writes the RMSD distribution.
-
-
-.B -ev
-writes the eigenvectors of the RMSD matrix
-diagonalization.
-
-
-.B -sz
-writes the cluster sizes.
-
-
-.B -tr
-writes a matrix of the number transitions between
-cluster pairs.
-
-
-.B -ntr
-writes the total number of transitions to or from
-each cluster.
-
-
-.B -clid
-writes the cluster number as a function of time.
-
-
-.B -cl
-writes average (with option
-.B -av
-) or central
-structure of each cluster or writes numbered files with cluster members
-for a selected set of clusters (with option
-.B -wcl
-, depends on
-
-.B -nst
-and
-.B -rmsmin
-).
-
-.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 xml
-
-.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 "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- Only use frame when t MOD dt = first time (ps)
-
-.BI "-tu" " enum" " ps"
- Time unit:
-.B ps
-,
-.B fs
-,
-.B ns
-,
-.B us
-,
-.B ms
-or
-.B s
-
-
-.BI "-[no]w" "no "
- View output xvg, xpm, eps and pdb files
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.BI "-[no]dista" "no "
- Use RMSD of distances instead of RMS deviation
-
-.BI "-nlevels" " int" " 40"
- Discretize RMSD matrix in levels
-
-.BI "-cutoff" " real" " 0.1 "
- RMSD cut-off (nm) for two structures to be neighbor
-
-.BI "-[no]fit" "yes "
- Use least squares fitting before RMSD calculation
-
-.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:
-.B linkage
-,
-.B jarvis-patrick
-,
-.B monte-carlo
-,
-.B diagonalization
-or
-.B gromos
-
-
-.BI "-minstruct" " int" " 1"
- Minimum number of structures in cluster for coloring in the xpm file
-
-.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_clustsize_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_clustsize_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_clustsize_d\fP
-.BI "-f" " traj.xtc "
-.BI "-s" " topol.tpr "
-.BI "-n" " index.ndx "
-.BI "-o" " csize.xpm "
-.BI "-ow" " csizew.xpm "
-.BI "-nc" " nclust.xvg "
-.BI "-mc" " maxclust.xvg "
-.BI "-ac" " avclust.xvg "
-.BI "-hc" " histo-clust.xvg "
-.BI "-temp" " temp.xvg "
-.BI "-mcn" " maxclust.ndx "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-dt" " time "
-.BI "-tu" " enum "
-.BI "-[no]w" ""
-.BI "-[no]xvgr" ""
-.BI "-cut" " real "
-.BI "-[no]mol" ""
-.BI "-[no]pbc" ""
-.BI "-nskip" " int "
-.BI "-nlevels" " int "
-.BI "-ndf" " int "
-.BI "-rgblo" " vector "
-.BI "-rgbhi" " vector "
-.SH DESCRIPTION
-This program computes the size distributions of molecular/atomic clusters in
-the gas phase. The output is given in the form of a XPM file.
-The total number of clusters is written to a XVG file.
-
-
-When the
-.B -mol
-option is given clusters will be made out of
-molecules rather than atoms, which allows clustering of large molecules.
-In this case an index file would still contain atom numbers
-or your calculcation will die with a SEGV.
-
-
-When velocities are present in your trajectory, the temperature of
-the largest cluster will be printed in a separate xvg file assuming
-that the particles are free to move. If you are using constraints,
-please correct the temperature. For instance water simulated with SHAKE
-or SETTLE will yield a temperature that is 1.5 times too low. You can
-compensate for this with the -ndf option. Remember to take the removal
-of center of mass motion into account.
-
-
-The
-.B -mc
-option will produce an index file containing the
-atom numbers of the largest cluster.
-.SH FILES
-.BI "-f" " traj.xtc"
-.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
-
-.BI "-s" " topol.tpr"
-.B Input, Opt.
- Portable xdr run input file
-
-.BI "-n" " index.ndx"
-.B Input, Opt.
- Index file
-
-.BI "-o" " csize.xpm"
-.B Output
- X PixMap compatible matrix file
-
-.BI "-ow" " csizew.xpm"
-.B Output
- X PixMap compatible matrix file
-
-.BI "-nc" " nclust.xvg"
-.B Output
- xvgr/xmgr file
-
-.BI "-mc" " maxclust.xvg"
-.B Output
- xvgr/xmgr file
-
-.BI "-ac" " avclust.xvg"
-.B Output
- xvgr/xmgr file
-
-.BI "-hc" " histo-clust.xvg"
-.B Output
- xvgr/xmgr file
-
-.BI "-temp" " temp.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.BI "-mcn" " maxclust.ndx"
-.B Output, Opt.
- Index file
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- Only use frame when t MOD dt = first time (ps)
-
-.BI "-tu" " enum" " ps"
- Time unit:
-.B ps
-,
-.B fs
-,
-.B ns
-,
-.B us
-,
-.B ms
-or
-.B s
-
-
-.BI "-[no]w" "no "
- View output xvg, xpm, eps and pdb files
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.BI "-cut" " real" " 0.35 "
- Largest distance (nm) to be considered in a cluster
-
-.BI "-[no]mol" "no "
- Cluster molecules rather than atoms (needs tpr file)
-
-.BI "-[no]pbc" "yes "
- Use periodic boundary conditions
-
-.BI "-nskip" " int" " 0"
- Number of frames to skip between writing
-
-.BI "-nlevels" " int" " 20"
- Number of levels of grey in xpm output
-
-.BI "-ndf" " int" " -1"
- Number of degrees of freedom of the entire system for temperature calculation. If not set the number of atoms times three is used.
-
-.BI "-rgblo" " vector" " 1 1 0"
- RGB values for the color of the lowest occupied cluster size
-
-.BI "-rgbhi" " vector" " 0 0 1"
- RGB values for the color of the highest occupied cluster size
-
+++ /dev/null
-.TH g_confrms_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_confrms_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_confrms_d\fP
-.BI "-f1" " conf1.gro "
-.BI "-f2" " conf2.gro "
-.BI "-o" " fit.pdb "
-.BI "-n1" " fit1.ndx "
-.BI "-n2" " fit2.ndx "
-.BI "-no" " match.ndx "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-[no]w" ""
-.BI "-[no]one" ""
-.BI "-[no]mw" ""
-.BI "-[no]pbc" ""
-.BI "-[no]fit" ""
-.BI "-[no]name" ""
-.BI "-[no]label" ""
-.BI "-[no]bfac" ""
-.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.
-With
-.B -name
-only matching atom names from the selected groups
-will be used for the fit and RMSD calculation. This can be useful
-when comparing mutants of a protein.
-
-
-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
-). Also in a
-.B .pdb
-file, B-factors
-calculated from the atomic MSD values can be written with
-.B -bfac
-.
-.SH FILES
-.BI "-f1" " conf1.gro"
-.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
-
-.BI "-f2" " conf2.gro"
-.B Input
- Generic structure: gro g96 pdb tpr tpb tpa xml
-
-.BI "-o" " fit.pdb"
-.B Output
- Generic structure: gro g96 pdb xml
-
-.BI "-n1" " fit1.ndx"
-.B Input, Opt.
- Index file
-
-.BI "-n2" " fit2.ndx"
-.B Input, Opt.
- Index file
-
-.BI "-no" " match.ndx"
-.B Output, Opt.
- Index file
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-[no]w" "no "
- View output xvg, xpm, eps and pdb files
-
-.BI "-[no]one" "no "
- Only write the fitted structure to file
-
-.BI "-[no]mw" "yes "
- Mass-weighted fitting and RMSD
-
-.BI "-[no]pbc" "no "
- Try to make molecules whole again
-
-.BI "-[no]fit" "yes "
- Do least squares superposition of the target structure to the reference
-
-.BI "-[no]name" "no "
- Only compare matching atom names
-
-.BI "-[no]label" "no "
- Added chain labels A for first and B for second structure
-
-.BI "-[no]bfac" "no "
- Output B-factors from atomic MSD values
-
+++ /dev/null
-.TH g_covar_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_covar_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_covar_d\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 "-ascii" " covar.dat "
-.BI "-xpm" " covar.xpm "
-.BI "-xpma" " covara.xpm "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-dt" " time "
-.BI "-tu" " enum "
-.BI "-[no]xvgr" ""
-.BI "-[no]fit" ""
-.BI "-[no]ref" ""
-.BI "-[no]mwa" ""
-.BI "-last" " int "
-.BI "-[no]pbc" ""
-.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
-.
-
-
-
-Option
-.B -ascii
-writes the whole covariance matrix to
-an ASCII file. The order of the elements is: x1x1, x1y1, x1z1, x1x2, ...
-
-
-
-Option
-.B -xpm
-writes the whole covariance matrix to an xpm file.
-
-
-
-Option
-.B -xpma
-writes the atomic covariance matrix to an xpm file,
-i.e. for each atom pair the sum of the xx, yy and zz covariances is
-written.
-.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 xml
-
-.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 xml
-
-.BI "-l" " covar.log"
-.B Output
- Log file
-
-.BI "-ascii" " covar.dat"
-.B Output, Opt.
- Generic data file
-
-.BI "-xpm" " covar.xpm"
-.B Output, Opt.
- X PixMap compatible matrix file
-
-.BI "-xpma" " covara.xpm"
-.B Output, Opt.
- X PixMap compatible matrix file
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- Only use frame when t MOD dt = first time (ps)
-
-.BI "-tu" " enum" " ps"
- Time unit:
-.B ps
-,
-.B fs
-,
-.B ns
-,
-.B us
-,
-.B ms
-or
-.B s
-
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.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)
-
-.BI "-[no]pbc" "yes "
- Apply corrections for periodic boundary conditions
-
+++ /dev/null
-.TH g_density_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_density_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_density_d\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 "-nice" " int "
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-dt" " time "
-.BI "-[no]w" ""
-.BI "-[no]xvgr" ""
-.BI "-d" " string "
-.BI "-sl" " int "
-.BI "-dens" " enum "
-.BI "-ng" " int "
-.BI "-[no]symm" ""
-.BI "-[no]center" ""
-.SH DESCRIPTION
-Compute partial densities across the box, using an index file. Densities
-in kg/m3, number densities or electron densities can be
-calculated. For electron densities, a file describing the number of
-electrons for each type of atom should be provided using
-.B -ei
-.
-It should look like:
-
- 2
-
- atomname = nrelectrons
-
- atomname = nrelectrons
-
-The first line contains the number of lines to read from the file.
-There should be one line for each unique atom name in your system.
-The number of electrons for each atom is modified 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 xml
-
-.BI "-ei" " electrons.dat"
-.B Input, Opt.
- 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 "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- Only use frame when t MOD dt = first time (ps)
-
-.BI "-[no]w" "no "
- View output xvg, xpm, eps and pdb files
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.BI "-d" " string" " Z"
- Take the normal on the membrane in direction X, Y or Z.
-
-.BI "-sl" " int" " 50"
- Divide the box in nr slices.
-
-.BI "-dens" " enum" " mass"
- Density:
-.B mass
-,
-.B number
-,
-.B charge
-or
-.B electron
-
-
-.BI "-ng" " int" " 1"
- Number of groups to compute densities of
-
-.BI "-[no]symm" "no "
- Symmetrize the density along the axis, with respect to the center. Useful for bilayers.
-
-.BI "-[no]center" "no "
- Shift the center of mass along the axis to zero. This means if your axis is Z and your box is bX, bY, bZ, the center of mass will be at bX/2, bY/2, 0.
-
-.SH KNOWN PROBLEMS
-\- When calculating electron densities, atomnames are used instead of types. This is bad.
-
+++ /dev/null
-.TH g_densmap_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_densmap_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_densmap_d\fP
-.BI "-f" " traj.xtc "
-.BI "-s" " topol.tpr "
-.BI "-n" " index.ndx "
-.BI "-o" " densmap.xpm "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-dt" " time "
-.BI "-[no]w" ""
-.BI "-bin" " real "
-.BI "-aver" " enum "
-.BI "-xmin" " real "
-.BI "-xmax" " real "
-.BI "-n1" " int "
-.BI "-n2" " int "
-.BI "-amax" " real "
-.BI "-rmax" " real "
-.BI "-[no]mirror" ""
-.BI "-unit" " enum "
-.BI "-dmin" " real "
-.BI "-dmax" " real "
-.SH DESCRIPTION
-g_densmap computes 2D number-density maps.
-It can make planar and axial-radial density maps.
-The output
-.B .xpm
-file can be visualized with for instance xv
-and can be converted to postscript with xpm2ps.
-
-
-
-The default analysis is a 2-D number-density map for a selected
-group of atoms in the x-y plane.
-The averaging direction can be changed with the option
-.B -aver
-.
-When
-.B -xmin
-and/or
-.B -xmax
-are set only atoms that are
-within the limit(s) in the averaging direction are taken into account.
-The grid spacing is set with the option
-.B -bin
-.
-When
-.B -n1
-or
-.B -n2
-is non-zero, the grid
-size is set by this option.
-Box size fluctuations are properly taken into account.
-
-
-
-When options
-.B -amax
-and
-.B -rmax
-are set, an axial-radial
-number-density map is made. Three groups should be supplied, the centers
-of mass of the first two groups define the axis, the third defines the
-analysis group. The axial direction goes from -amax to +amax, where
-the center is defined as the midpoint between the centers of mass and
-the positive direction goes from the first to the second center of mass.
-The radial direction goes from 0 to rmax or from -rmax to +rmax
-when the
-.B -mirror
-option has been set.
-
-
-
-The normalization of the output is set with the
-.B -unit
-option.
-The default produces a true number density. Unit
-.B nm-2
-leaves out
-the normalization for the averaging or the angular direction.
-Option
-.B count
-produces the count for each grid cell.
-When you do not want the scale in the output to go
-from zero to the maximum density, you can set the maximum
-with the option
-.B -dmax
-.
-.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 xml
-
-.BI "-n" " index.ndx"
-.B Input, Opt.
- Index file
-
-.BI "-o" " densmap.xpm"
-.B Output
- X PixMap compatible matrix file
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- 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" " 0.02 "
- Grid size (nm)
-
-.BI "-aver" " enum" " z"
- The direction to average over:
-.B z
-,
-.B y
-or
-.B x
-
-
-.BI "-xmin" " real" " -1 "
- Minimum coordinate for averaging
-
-.BI "-xmax" " real" " -1 "
- Maximum coordinate for averaging
-
-.BI "-n1" " int" " 0"
- Number of grid cells in the first direction
-
-.BI "-n2" " int" " 0"
- Number of grid cells in the second direction
-
-.BI "-amax" " real" " 0 "
- Maximum axial distance from the center
-
-.BI "-rmax" " real" " 0 "
- Maximum radial distance
-
-.BI "-[no]mirror" "no "
- Add the mirror image below the axial axis
-
-.BI "-unit" " enum" " nm-3"
- Unit for the output:
-.B nm-3
-,
-.B nm-2
-or
-.B count
-
-
-.BI "-dmin" " real" " 0 "
- Minimum density in output
-
-.BI "-dmax" " real" " 0 "
- Maximum density in output (0 means calculate it)
-
+++ /dev/null
-.TH g_dielectric_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_dielectric_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_dielectric_d\fP
-.BI "-f" " dipcorr.xvg "
-.BI "-d" " deriv.xvg "
-.BI "-o" " epsw.xvg "
-.BI "-c" " cole.xvg "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-dt" " time "
-.BI "-[no]w" ""
-.BI "-[no]xvgr" ""
-.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" " dipcorr.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 "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- Only use frame when t MOD dt = first time (ps)
-
-.BI "-[no]w" "no "
- View output xvg, xpm, eps and pdb files
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.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:
-.B none
-,
-.B exp
-,
-.B aexp
-,
-.B exp_exp
-,
-.B vac
-,
-.B exp5
-,
-.B exp7
-or
-.B exp9
-
-
-.BI "-nsmooth" " int" " 3"
- Number of points for smoothing
-
+++ /dev/null
-.TH g_dih_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_dih_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_dih_d\fP
-.BI "-f" " traj.xtc "
-.BI "-s" " topol.tpr "
-.BI "-o" " hello.out "
-.BI "-[no]h" ""
-.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 xml
-
-.BI "-o" " hello.out"
-.B Output
- Generic output file
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- 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)
-
+++ /dev/null
-.TH g_dipoles_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_dipoles_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_dipoles_d\fP
-.BI "-enx" " ener.edr "
-.BI "-f" " traj.xtc "
-.BI "-s" " topol.tpr "
-.BI "-n" " index.ndx "
-.BI "-o" " Mtot.xvg "
-.BI "-eps" " epsilon.xvg "
-.BI "-a" " aver.xvg "
-.BI "-d" " dipdist.xvg "
-.BI "-c" " dipcorr.xvg "
-.BI "-g" " gkr.xvg "
-.BI "-adip" " adip.xvg "
-.BI "-dip3d" " dip3d.xvg "
-.BI "-cos" " cosaver.xvg "
-.BI "-cmap" " cmap.xpm "
-.BI "-q" " quadrupole.xvg "
-.BI "-slab" " slab.xvg "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-dt" " time "
-.BI "-[no]w" ""
-.BI "-[no]xvgr" ""
-.BI "-mu" " real "
-.BI "-mumax" " real "
-.BI "-epsilonRF" " real "
-.BI "-skip" " int "
-.BI "-temp" " real "
-.BI "-corr" " enum "
-.BI "-[no]pairs" ""
-.BI "-ncos" " int "
-.BI "-[no]pbc" ""
-.BI "-axis" " string "
-.BI "-sl" " int "
-.BI "-gkratom" " int "
-.BI "-gkratom2" " int "
-.BI "-rcmax" " real "
-.BI "-[no]phi" ""
-.BI "-nlevels" " int "
-.BI "-ndegrees" " 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.
-For molecules with a net charge, the net charge is subtracted at
-center of mass of the molecule.
-
-
-The file Mtot.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 dipdist.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 -corr is used. The output file name is given with the
-.B -c
-
-option.
-The correlation functions can be averaged over all molecules
-(
-.B mol
-), plotted per molecule seperately (
-.B molsep
-)
-or it can be computed over the total dipole moment of the simulation box
-(
-.B total
-).
-
-
-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. In the same plot
-we also include the energy per scale computed by taking the inner product of
-the dipoles divided by the distance to the third power.
-
-
-
-
-
-EXAMPLES
-
-
-g_dipoles -corr mol -P1 -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 xml
-
-.BI "-n" " index.ndx"
-.B Input, Opt.
- Index file
-
-.BI "-o" " Mtot.xvg"
-.B Output
- xvgr/xmgr file
-
-.BI "-eps" " 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 "-adip" " adip.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.BI "-dip3d" " dip3d.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.BI "-cos" " cosaver.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.BI "-cmap" " cmap.xpm"
-.B Output, Opt.
- X PixMap compatible matrix file
-
-.BI "-q" " quadrupole.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.BI "-slab" " slab.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- Only use frame when t MOD dt = first time (ps)
-
-.BI "-[no]w" "no "
- View output xvg, xpm, eps and pdb files
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.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 "-corr" " enum" " none"
- Correlation function to calculate:
-.B none
-,
-.B mol
-,
-.B molsep
-or
-.B total
-
-
-.BI "-[no]pairs" "yes "
- Calculate |cos theta| between all pairs of molecules. May be slow
-
-.BI "-ncos" " int" " 1"
- Must be 1 or 2. Determines whether the cos is computed between all mole cules in one group, or between molecules in two different groups. This turns on the -gkr flag.
-
-.BI "-[no]pbc" "yes "
- Use periodic boundary conditions
-
-.BI "-axis" " string" " Z"
- Take the normal on the computational box in direction X, Y or Z.
-
-.BI "-sl" " int" " 10"
- Divide the box in nr slices.
-
-.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 "-gkratom2" " int" " 0"
- Same as previous option in case ncos = 2, i.e. dipole interaction between two groups of molecules
-
-.BI "-rcmax" " real" " 0 "
- Maximum distance to use in the dipole orientation distribution (with ncos == 2). If zero, a criterium based on the box length will be used.
-
-.BI "-[no]phi" "no "
- Plot the 'torsion angle' defined as the rotation of the two dipole vectors around the distance vector between the two molecules in the xpm file from the -cmap option. By default the cosine of the angle between the dipoles is plotted.
-
-.BI "-nlevels" " int" " 20"
- Number of colors in the cmap output
-
-.BI "-ndegrees" " int" " 90"
- Number of divisions on the y-axis in the camp output (for 180 degrees)
-
-.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):
-.B 0
-,
-.B 1
-,
-.B 2
-or
-.B 3
-
-
-.BI "-fitfn" " enum" " none"
- Fit function:
-.B none
-,
-.B exp
-,
-.B aexp
-,
-.B exp_exp
-,
-.B vac
-,
-.B exp5
-,
-.B exp7
-or
-.B exp9
-
-
-.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_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_disre_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_disre_d\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 "-q" " viol.pdb "
-.BI "-c" " clust.ndx "
-.BI "-x" " matrix.xpm "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-dt" " time "
-.BI "-[no]w" ""
-.BI "-[no]xvgr" ""
-.BI "-ntop" " int "
-.BI "-maxdr" " real "
-.BI "-nlevels" " int "
-.BI "-[no]third" ""
-.SH DESCRIPTION
-g_disre computes violations of distance restraints.
-If necessary all protons can be added to a protein molecule
-using the protonate program.
-
-
-The program always
-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. However,
-the time averaged values per restraint are given in the log file.
-
-
-An index file may be used to select specific restraints for
-printing.
-
-
-When the optional
-.B -q
-flag is given a pdb file coloured by the
-amount of average violations.
-
-
-When the
-.B -c
-option is given, an index file will be read
-containing the frames in your trajectory corresponding to the clusters
-(defined in another manner) that you want to analyze. For these clusters
-the program will compute average violations using the third power
-averaging algorithm and print them in the log file.
-.SH FILES
-.BI "-s" " topol.tpr"
-.B Input
- Generic run input: tpr tpb tpa xml
-
-.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
-
-.BI "-q" " viol.pdb"
-.B Output, Opt.
- Protein data bank file
-
-.BI "-c" " clust.ndx"
-.B Input, Opt.
- Index file
-
-.BI "-x" " matrix.xpm"
-.B Output, Opt.
- X PixMap compatible matrix file
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- Only use frame when t MOD dt = first time (ps)
-
-.BI "-[no]w" "no "
- View output xvg, xpm, eps and pdb files
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.BI "-ntop" " int" " 0"
- Number of large violations that are stored in the log file every step
-
-.BI "-maxdr" " real" " 0 "
- Maximum distance violation in matrix output. If less than or equal to 0 the maximum will be determined by the data.
-
-.BI "-nlevels" " int" " 20"
- Number of levels in the matrix output
-
-.BI "-[no]third" "yes "
- Use inverse third power averaging or linear for matrix output
-
+++ /dev/null
-.TH g_dist_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_dist_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_dist_d\fP
-.BI "-f" " traj.xtc "
-.BI "-s" " topol.tpr "
-.BI "-n" " index.ndx "
-.BI "-o" " dist.xvg "
-.BI "-lt" " lifetime.xvg "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-dt" " time "
-.BI "-[no]xvgr" ""
-.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.
-
-
-With options
-.B -lt
-and
-.B -dist
-the number of contacts
-of all atoms in group 2 that are closer than a certain distance
-to the center of mass of group 1 are plotted as a function of the time
-that the contact was continously present.
-
-
-Other programs that calculate distances are
-.B g_mindist
-
-and
-.B g_bond
-.
-.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 xml
-
-.BI "-n" " index.ndx"
-.B Input, Opt.
- Index file
-
-.BI "-o" " dist.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.BI "-lt" " lifetime.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- Only use frame when t MOD dt = first time (ps)
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.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_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_dyndom_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_dyndom_d\fP
-.BI "-f" " dyndom.pdb "
-.BI "-o" " rotated.xtc "
-.BI "-n" " domains.ndx "
-.BI "-[no]h" ""
-.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://www.cmp.uea.ac.uk/dyndom/
-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 "-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_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_enemat_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_enemat_d\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 "-nice" " int "
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-dt" " time "
-.BI "-[no]w" ""
-.BI "-[no]xvgr" ""
-.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]lj" ""
-.BI "-[no]lj14" ""
-.BI "-[no]bhamsr" ""
-.BI "-[no]bhamlr" ""
-.BI "-[no]free" ""
-.BI "-temp" " real "
-.SH DESCRIPTION
-g_enemat extracts an energy matrix from the energy file (
-.B -f
-).
-With
-.B -groups
-a file must be supplied with on each
-line a group of atoms to be used. For these groups matrix of
-interaction energies will be extracted from the energy file
-by looking for energy groups with names corresponding to pairs
-of groups of atoms. E.g. if your
-.B -groups
-file contains:
-
-
-.B 2
-
-
-
-.B Protein
-
-
-
-.B SOL
-
-
-then energy groups with names like 'Coul-SR:Protein-SOL' and
-'LJ:Protein-SOL' are expected in the energy file (although
-
-.B g_enemat
-is most useful if many groups are analyzed
-simultaneously). Matrices for different energy types are written
-out separately, as controlled by the
-
-.B -[no]coul
-,
-.B -[no]coulr
-,
-.B -[no]coul14
-,
-
-.B -[no]lj
-,
-.B -[no]lj14
-,
-
-.B -[no]bham
-and
-.B -[no]free
-options.
-Finally, the total interaction energy energy per group can be
-calculated (
-.B -etot
-).
-
-
-An approximation of the free energy can be 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 "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- Only use frame when t MOD dt = first time (ps)
-
-.BI "-[no]w" "no "
- View output xvg, xpm, eps and pdb files
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.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 extracts 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 "
- extract Coulomb SR energies
-
-.BI "-[no]coulr" "no "
- extract Coulomb LR energies
-
-.BI "-[no]coul14" "no "
- extract Coulomb 1-4 energies
-
-.BI "-[no]lj" "yes "
- extract Lennard-Jones SR energies
-
-.BI "-[no]lj" "no "
- extract Lennard-Jones LR energies
-
-.BI "-[no]lj14" "no "
- extract Lennard-Jones 1-4 energies
-
-.BI "-[no]bhamsr" "no "
- extract Buckingham SR energies
-
-.BI "-[no]bhamlr" "no "
- extract Buckingham LR energies
-
-.BI "-[no]free" "yes "
- calculate free energy
-
-.BI "-temp" " real" " 300 "
- reference temperature for free energy calculation
-
+++ /dev/null
-.TH g_energy_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_energy_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_energy_d\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 "-ora" " orienta.xvg "
-.BI "-ort" " orientt.xvg "
-.BI "-oda" " orideva.xvg "
-.BI "-odr" " oridevr.xvg "
-.BI "-odt" " oridevt.xvg "
-.BI "-oten" " oriten.xvg "
-.BI "-corr" " enecorr.xvg "
-.BI "-vis" " visco.xvg "
-.BI "-ravg" " runavgdf.xvg "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-[no]w" ""
-.BI "-[no]xvgr" ""
-.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 "-[no]orinst" ""
-.BI "-[no]ovec" ""
-.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.
-
-
-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. The term fluctuation gives the RMSD around
-the LSQ fit.
-
-
-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.
-
-
-Options
-.B -ora
-,
-.B -ort
-,
-.B -oda
-,
-.B -odr
-and
-
-.B -odt
-are used for analyzing orientation restraint data.
-The first two options plot the orientation, the last three the
-deviations of the orientations from the experimental values.
-The options that end on an 'a' plot the average over time
-as a function of restraint. The options that end on a 't'
-prompt the user for restraint label numbers and plot the data
-as a function of time. Option
-.B -odr
-plots the RMS
-deviation as a function of restraint.
-When the run used time or ensemble averaged orientation restraints,
-option
-.B -orinst
-can be used to analyse the instantaneous,
-not ensemble-averaged orientations and deviations instead of
-the time and ensemble averages.
-
-
-Option
-.B -oten
-plots the eigenvalues of the molecular order
-tensor for each orientation restraint experiment. With option
-
-.B -ovec
-also the eigenvectors are plotted.
-
-
-With
-.B -fee
-an estimate is calculated for the free-energy
-difference with an ideal gas state:
-
- Delta A = A(N,V,T) - A_idgas(N,V,T) = kT ln e(Upot/kT)
-
- Delta G = G(N,p,T) - G_idgas(N,p,T) = kT ln e(Upot/kT)
-
-where k is Boltzmann's constant, T is set by
-.B -fetemp
-andthe 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:
-
- Delta S(N,V,T) = S(N,V,T) - S_idgas(N,V,T) = (Upot - Delta A)/T
-
- Delta S(N,p,T) = S(N,p,T) - S_idgas(N,p,T) = (Upot + pV - Delta G)/T
-
-
-
-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 xml
-
-.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 "-ora" " orienta.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.BI "-ort" " orientt.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.BI "-oda" " orideva.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.BI "-odr" " oridevr.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.BI "-odt" " oridevt.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.BI "-oten" " oriten.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 "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-[no]w" "no "
- View output xvg, xpm, eps and pdb files
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.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 "-[no]orinst" "no "
- Analyse instantaneous orientation data
-
-.BI "-[no]ovec" "no "
- Also plot the eigenvectors with -oten
-
-.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):
-.B 0
-,
-.B 1
-,
-.B 2
-or
-.B 3
-
-
-.BI "-fitfn" " enum" " none"
- Fit function:
-.B none
-,
-.B exp
-,
-.B aexp
-,
-.B exp_exp
-,
-.B vac
-,
-.B exp5
-,
-.B exp7
-or
-.B exp9
-
-
-.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_filter_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_filter_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_filter_d\fP
-.BI "-f" " traj.xtc "
-.BI "-s" " topol.tpr "
-.BI "-n" " index.ndx "
-.BI "-ol" " lowpass.xtc "
-.BI "-oh" " highpass.xtc "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-dt" " time "
-.BI "-[no]w" ""
-.BI "-nf" " int "
-.BI "-[no]all" ""
-.BI "-[no]nojump" ""
-.BI "-[no]fit" ""
-.SH DESCRIPTION
-g_filter performs frequency filtering on a trajectory.
-The filter shape is cos(pi t/A) + 1 from -A to +A, where A is given
-by the option
-.B -nf
-times the time step in the input trajectory.
-This filter reduces fluctuations with period A by 85%, with period
-2*A by 50% and with period 3*A by 17% for low-pass filtering.
-Both a low-pass and high-pass filtered trajectory can be written.
-
-
-Option
-.B -ol
-writes a low-pass filtered trajectory.
-A frame is written every
-.B nf
-input frames.
-This ratio of filter length and output interval ensures a good
-suppression of aliasing of high-frequency motion, which is useful for
-making smooth movies. Also averages of properties which are linear
-in the coordinates are preserved, since all input frames are weighted
-equally in the output.
-When all frames are needed, use the
-.B -all
-option.
-
-
-Option
-.B -oh
-writes a high-pass filtered trajectory.
-The high-pass filtered coordinates are added to the coordinates
-from the structure file. When using high-pass filtering use
-.B -fit
-
-or make sure you use a trajectory which has been fitted on
-the coordinates in the structure file.
-.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 xml
-
-.BI "-n" " index.ndx"
-.B Input, Opt.
- Index file
-
-.BI "-ol" " lowpass.xtc"
-.B Output, Opt.
- Generic trajectory: xtc trr trj gro g96 pdb
-
-.BI "-oh" " highpass.xtc"
-.B Output, Opt.
- Generic trajectory: xtc trr trj gro g96 pdb
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- Only use frame when t MOD dt = first time (ps)
-
-.BI "-[no]w" "no "
- View output xvg, xpm, eps and pdb files
-
-.BI "-nf" " int" " 10"
- Sets the filter length as well as the output interval for low-pass filtering
-
-.BI "-[no]all" "no "
- Write all low-pass filtered frames
-
-.BI "-[no]nojump" "yes "
- Remove jumps of atoms across the box
-
-.BI "-[no]fit" "no "
- Fit all frames to a reference structure
-
+++ /dev/null
-.TH g_gyrate_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_gyrate_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_gyrate_d\fP
-.BI "-f" " traj.xtc "
-.BI "-s" " topol.tpr "
-.BI "-n" " index.ndx "
-.BI "-o" " gyrate.xvg "
-.BI "-acf" " moi-acf.xvg "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-dt" " time "
-.BI "-[no]w" ""
-.BI "-[no]xvgr" ""
-.BI "-nmol" " int "
-.BI "-[no]q" ""
-.BI "-[no]p" ""
-.BI "-[no]moi" ""
-.BI "-nz" " 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_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.
-
-
-With the
-.B -nmol
-option the radius of gyration will be calculated
-for multiple molecules by splitting the analysis group in equally
-sized parts.
-
-
-With the option
-.B -nz
-2D radii of gyration in the x-y plane
-of slices along the z-axis are calculated.
-.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 xml
-
-.BI "-n" " index.ndx"
-.B Input, Opt.
- Index file
-
-.BI "-o" " gyrate.xvg"
-.B Output
- xvgr/xmgr file
-
-.BI "-acf" " moi-acf.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- Only use frame when t MOD dt = first time (ps)
-
-.BI "-[no]w" "no "
- View output xvg, xpm, eps and pdb files
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.BI "-nmol" " int" " 1"
- The number of molecules to analyze
-
-.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.
-
-.BI "-[no]moi" "no "
- Calculate the moments of inertia (defined by the principal axes).
-
-.BI "-nz" " int" " 0"
- Calculate the 2D radii of gyration of slices along the z-axis
-
-.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):
-.B 0
-,
-.B 1
-,
-.B 2
-or
-.B 3
-
-
-.BI "-fitfn" " enum" " none"
- Fit function:
-.B none
-,
-.B exp
-,
-.B aexp
-,
-.B exp_exp
-,
-.B vac
-,
-.B exp5
-,
-.B exp7
-or
-.B exp9
-
-
-.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_h2order_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_h2order_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_h2order_d\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 "-nice" " int "
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-dt" " time "
-.BI "-[no]w" ""
-.BI "-[no]xvgr" ""
-.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 xml
-
-.BI "-o" " order.xvg"
-.B Output
- xvgr/xmgr file
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- Only use frame when t MOD dt = first time (ps)
-
-.BI "-[no]w" "no "
- View output xvg, xpm, eps and pdb files
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.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 KNOWN PROBLEMS
-\- 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_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_hbond_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_hbond_d\fP
-.BI "-f" " traj.xtc "
-.BI "-s" " topol.tpr "
-.BI "-n" " index.ndx "
-.BI "-num" " hbnum.xvg "
-.BI "-g" " hbond.log "
-.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 "-don" " donor.xvg "
-.BI "-dan" " danum.xvg "
-.BI "-life" " hblife.xvg "
-.BI "-nhbdist" " nhbdist.xvg "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-dt" " time "
-.BI "-[no]xvgr" ""
-.BI "-[no]ins" ""
-.BI "-a" " real "
-.BI "-r" " real "
-.BI "-[no]da" ""
-.BI "-abin" " real "
-.BI "-rbin" " real "
-.BI "-[no]nitacc" ""
-.BI "-[no]contact" ""
-.BI "-shell" " real "
-.BI "-fitstart" " real "
-.BI "-temp" " real "
-.BI "-smooth" " real "
-.BI "-dump" " int "
-.BI "-max_hb" " real "
-.BI "-[no]merge" ""
-.BI "-acflen" " int "
-.BI "-[no]normalize" ""
-.BI "-P" " enum "
-.BI "-fitfn" " enum "
-.BI "-ncskip" " int "
-.BI "-beginfit" " real "
-.BI "-endfit" " real "
-.SH DESCRIPTION
-g_hbond computes and analyzes hydrogen bonds. Hydrogen bonds are
-determined based on cutoffs for the angle Acceptor - Donor - Hydrogen
-(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.
-
-
-.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 -dan
-: write out the number of donors and acceptors analyzed for
-each timeframe. This is especially usefull when using
-.B -shell
-.
-
-
-.B -nhbdist
-: compute the number of HBonds per hydrogen in order to
-compare results to Raman Spectroscopy.
-
-
-
-Note: options
-.B -ac
-,
-.B -life
-,
-.B -hbn
-and
-.B -hbm
-
-require an amount of memory proportional to the total numbers of donors
-times the total number of acceptors in the selected group(s).
-.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 xml
-
-.BI "-n" " index.ndx"
-.B Input, Opt.
- Index file
-
-.BI "-num" " hbnum.xvg"
-.B Output
- xvgr/xmgr file
-
-.BI "-g" " hbond.log"
-.B Output, Opt.
- Log 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 "-don" " donor.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.BI "-dan" " danum.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.BI "-life" " hblife.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.BI "-nhbdist" " nhbdist.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- Only use frame when t MOD dt = first time (ps)
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.BI "-[no]ins" "no "
- Analyze solvent insertion
-
-.BI "-a" " real" " 30 "
- Cutoff angle (degrees, Acceptor - Donor - Hydrogen)
-
-.BI "-r" " real" " 0.35 "
- Cutoff radius (nm, X - Acceptor, see next option)
-
-.BI "-[no]da" "yes "
- Use distance Donor-Acceptor (if TRUE) or Hydrogen-Acceptor (FALSE)
-
-.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 "-[no]contact" "no "
- Do not look for hydrogen bonds, but merely for contacts within the cut-off distance
-
-.BI "-shell" " real" " -1 "
- when 0, only calculate hydrogen bonds within nm shell around one particle
-
-.BI "-fitstart" " real" " 1 "
- Time (ps) from which to start fitting the correlation functions in order to obtain the forward and backward rate constants for HB breaking and formation
-
-.BI "-temp" " real" " 298.15"
- Temperature (K) for computing the Gibbs energy corresponding to HB breaking and reforming
-
-.BI "-smooth" " real" " -1 "
- If = 0, the tail of the ACF will be smoothed by fitting it to an exponential function: y = A exp(-x/tau)
-
-.BI "-dump" " int" " 0"
- Dump the first N hydrogen bond ACFs in a single xvg file for debugging
-
-.BI "-max_hb" " real" " 0 "
- Theoretical maximum number of hydrogen bonds used for normalizing HB autocorrelation function. Can be useful in case the program estimates it wrongly
-
-.BI "-[no]merge" "yes "
- H-bonds between the same donor and acceptor, but with different hydrogen are treated as a single H-bond. Mainly important for the ACF.
-
-.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):
-.B 0
-,
-.B 1
-,
-.B 2
-or
-.B 3
-
-
-.BI "-fitfn" " enum" " none"
- Fit function:
-.B none
-,
-.B exp
-,
-.B aexp
-,
-.B exp_exp
-,
-.B vac
-,
-.B exp5
-,
-.B exp7
-or
-.B exp9
-
-
-.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 KNOWN PROBLEMS
-\- The option
-.B -sel
-that used to work on selected hbonds is out of order, and therefore not available for the time being.
-
+++ /dev/null
-.TH g_helix_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_helix_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_helix_d\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 "-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 "-prop" " enum "
-.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 xml
-
-.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 xml
-
-.BI "-co" " waver.gro"
-.B Output
- Generic structure: gro g96 pdb xml
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- 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 "-prop" " enum" " RAD"
- Select property to weight eigenvectors with. WARNING experimental stuff:
-.B RAD
-,
-.B TWIST
-,
-.B RISE
-,
-.B LEN
-,
-.B NHX
-,
-.B DIP
-,
-.B RMS
-,
-.B CPHI
-,
-.B RMSA
-,
-.B PHI
-,
-.B PSI
-,
-.B HB3
-,
-.B HB4
-,
-.B HB5
-or
-.B CD222
-
-
-.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_kinetics_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_kinetics_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_kinetics_d\fP
-.BI "-f" " temp.xvg "
-.BI "-d" " data.xvg "
-.BI "-d2" " data2.xvg "
-.BI "-o" " ft_all.xvg "
-.BI "-o2" " it_all.xvg "
-.BI "-o3" " ft_repl.xvg "
-.BI "-ee" " err_est.xvg "
-.BI "-g" " remd.log "
-.BI "-m" " melt.xvg "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-tu" " enum "
-.BI "-[no]w" ""
-.BI "-[no]xvgr" ""
-.BI "-[no]time" ""
-.BI "-b" " real "
-.BI "-e" " real "
-.BI "-bfit" " real "
-.BI "-efit" " real "
-.BI "-T" " real "
-.BI "-n" " int "
-.BI "-cut" " real "
-.BI "-ucut" " real "
-.BI "-euf" " real "
-.BI "-efu" " real "
-.BI "-ei" " real "
-.BI "-maxiter" " int "
-.BI "-[no]back" ""
-.BI "-tol" " real "
-.BI "-skip" " int "
-.BI "-[no]split" ""
-.BI "-[no]sum" ""
-.BI "-[no]discrete" ""
-.BI "-mult" " int "
-.SH DESCRIPTION
-g_kinetics reads two xvg files, each one containing data for N replicas.
-The first file contains the temperature of each replica at each timestep,and the second contains real values that can be interpreted as
-an indicator for folding. If the value in the file is larger than
-the cutoff it is taken to be unfolded and the other way around.
-
-
-From these data an estimate of the forward and backward rate constants
-for folding is made at a reference temperature. In addition,a theoretical melting curve and free energy as a function of temperatureare printed in an xvg file.
-
-
-The user can give a max value to be regarded as intermediate
-(
-.B -ucut
-), which, when given will trigger the use of an intermediate state
-in the algorithm to be defined as those structures that have
-cutoff DATA ucut. Structures with DATA values larger than ucut will
-not be regarded as potential folders. In this case 8 parameters are optimized.
-
-
-The average fraction foled is printed in an xvg file together with the fit to it.
-If an intermediate is used a further file will show the build of the intermediate and the fit to that process.
-
-
-The program can also be used with continuous variables (by setting
-
-.B -nodiscrete
-). In this case kinetics of other processes can be
-studied. This is very much a work in progress and hence the manual
-(this information) is lagging behind somewhat.
-
-
-In order to compile this program you need access to the GNU
-scientific library.
-.SH FILES
-.BI "-f" " temp.xvg"
-.B Input
- xvgr/xmgr file
-
-.BI "-d" " data.xvg"
-.B Input
- xvgr/xmgr file
-
-.BI "-d2" " data2.xvg"
-.B Input, Opt.
- xvgr/xmgr file
-
-.BI "-o" " ft_all.xvg"
-.B Output
- xvgr/xmgr file
-
-.BI "-o2" " it_all.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.BI "-o3" " ft_repl.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.BI "-ee" " err_est.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.BI "-g" " remd.log"
-.B Output
- Log file
-
-.BI "-m" " melt.xvg"
-.B Output
- xvgr/xmgr file
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-tu" " enum" " ps"
- Time unit:
-.B ps
-,
-.B fs
-,
-.B ns
-,
-.B us
-,
-.B ms
-or
-.B s
-
-
-.BI "-[no]w" "no "
- View output xvg, xpm, eps and pdb files
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.BI "-[no]time" "yes "
- Expect a time in the input
-
-.BI "-b" " real" " 0 "
- First time to read from set
-
-.BI "-e" " real" " 0 "
- Last time to read from set
-
-.BI "-bfit" " real" " -1 "
- Time to start the fit from
-
-.BI "-efit" " real" " -1 "
- Time to end the fit
-
-.BI "-T" " real" " 298.15"
- Reference temperature for computing rate constants
-
-.BI "-n" " int" " 1"
- Read data for replicas. Only necessary when files are written in xmgrace format using @type and & as delimiters.
-
-.BI "-cut" " real" " 0.2 "
- Cut-off (max) value for regarding a structure as folded
-
-.BI "-ucut" " real" " 0 "
- Cut-off (max) value for regarding a structure as intermediate (if not folded)
-
-.BI "-euf" " real" " 10 "
- Initial guess for energy of activation for folding (kJ/mole)
-
-.BI "-efu" " real" " 30 "
- Initial guess for energy of activation for unfolding (kJ/mole)
-
-.BI "-ei" " real" " 10 "
- Initial guess for energy of activation for intermediates (kJ/mole)
-
-.BI "-maxiter" " int" " 100"
- Max number of iterations
-
-.BI "-[no]back" "yes "
- Take the back reaction into account
-
-.BI "-tol" " real" " 0.001 "
- Absolute tolerance for convergence of the Nelder and Mead simplex algorithm
-
-.BI "-skip" " int" " 0"
- Skip points in the output xvg file
-
-.BI "-[no]split" "yes "
- Estimate error by splitting the number of replicas in two and refitting
-
-.BI "-[no]sum" "yes "
- Average folding before computing chi2
-
-.BI "-[no]discrete" "yes "
- Use a discrete folding criterium (F - U) or a continuous one
-
-.BI "-mult" " int" " 1"
- Factor to multiply the data with before discretization
-
+++ /dev/null
-.TH g_lie_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_lie_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_lie_d\fP
-.BI "-f" " ener.edr "
-.BI "-o" " lie.xvg "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-dt" " time "
-.BI "-[no]w" ""
-.BI "-[no]xvgr" ""
-.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 "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- Only use frame when t MOD dt = first time (ps)
-
-.BI "-[no]w" "no "
- View output xvg, xpm, eps and pdb files
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.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" " 0.5 "
- Factor in the LIE equation for Coulomb component of energy
-
-.BI "-ligand" " string" " none"
- Name of the ligand in the energy file
-
+++ /dev/null
-.TH g_mdmat_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_mdmat_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_mdmat_d\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 "-nice" " int "
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-dt" " time "
-.BI "-[no]xvgr" ""
-.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 xml
-
-.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 "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- Only use frame when t MOD dt = first time (ps)
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.BI "-t" " real" " 1.5 "
- trunc distance
-
-.BI "-nlevels" " int" " 40"
- Discretize distance in levels
-
+++ /dev/null
-.TH g_mindist_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_mindist_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_mindist_d\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 "-ox" " mindist.xtc "
-.BI "-or" " mindistres.xvg "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-dt" " time "
-.BI "-tu" " enum "
-.BI "-[no]w" ""
-.BI "-[no]xvgr" ""
-.BI "-[no]matrix" ""
-.BI "-[no]max" ""
-.BI "-d" " real "
-.BI "-[no]pi" ""
-.BI "-[no]split" ""
-.BI "-ng" " int "
-.BI "-[no]pbc" ""
-.SH DESCRIPTION
-g_mindist computes the distance between one group and a number of
-other groups. Both the minimum distance
-(between any pair of atoms from the respective groups)
-and the number of contacts within a given
-distance are written to two separate output files.
-With
-.B -or
-, minimum distances to each residue in the first
-group are determined and plotted as a function of reisdue number.
-
-
-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.
-
-
-Other programs that calculate distances are
-.B g_dist
-
-and
-.B g_bond
-.
-.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 xml
-
-.BI "-n" " index.ndx"
-.B Input, Opt.
- Index file
-
-.BI "-od" " mindist.xvg"
-.B Output
- xvgr/xmgr file
-
-.BI "-on" " numcont.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.BI "-o" " atm-pair.out"
-.B Output, Opt.
- Generic output file
-
-.BI "-ox" " mindist.xtc"
-.B Output, Opt.
- Generic trajectory: xtc trr trj gro g96 pdb
-
-.BI "-or" " mindistres.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- Only use frame when t MOD dt = first time (ps)
-
-.BI "-tu" " enum" " ps"
- Time unit:
-.B ps
-,
-.B fs
-,
-.B ns
-,
-.B us
-,
-.B ms
-or
-.B s
-
-
-.BI "-[no]w" "no "
- View output xvg, xpm, eps and pdb files
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.BI "-[no]matrix" "no "
- Calculate half a matrix of group-group distances
-
-.BI "-[no]max" "no "
- Calculate *maximum* distance instead of minimum
-
-.BI "-d" " real" " 0.6 "
- Distance for contacts
-
-.BI "-[no]pi" "no "
- Calculate minimum distance with periodic images
-
-.BI "-[no]split" "no "
- Split graph where time is zero
-
-.BI "-ng" " int" " 1"
- Number of secondary groups to compute distance to a central group
-
-.BI "-[no]pbc" "yes "
- Take periodic boundary conditions into account
-
+++ /dev/null
-.TH g_morph_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_morph_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_morph_d\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 "-nice" " int "
-.BI "-[no]w" ""
-.BI "-[no]xvgr" ""
-.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 xml
-
-.BI "-f2" " conf2.gro"
-.B Input
- Generic structure: gro g96 pdb tpr tpb tpa xml
-
-.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 "-nice" " int" " 0"
- Set the nicelevel
-
-.BI "-[no]w" "no "
- View output xvg, xpm, eps and pdb files
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.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_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_msd_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_msd_d\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 "-nice" " int "
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-dt" " time "
-.BI "-tu" " enum "
-.BI "-[no]w" ""
-.BI "-[no]xvgr" ""
-.BI "-type" " enum "
-.BI "-lateral" " enum "
-.BI "-ngroup" " int "
-.BI "-[no]mw" ""
-.BI "-[no]rmcomm" ""
-.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 time between additional starting points for the MSD calculation
-is set with
-.B -trestart
-.
-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.
-
-
-With option
-.B -rmcomm
-center of mass motion can be removed.
-For trajectories produced with GROMACS this is usually not necessary
-as mdrun usually already removes the center of mass motion.
-When you use this option be sure that the whole system is stored
-in the trajectory file.
-
-
-Option
-.B -mol
-plots the MSD for molecules, this implies
-
-.B -mw
-, i.e. for each inidividual molecule an diffusion constant
-is computed for its center of mass. 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 xml
-
-.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 "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- Only use frame when t MOD dt = first time (ps)
-
-.BI "-tu" " enum" " ps"
- Time unit:
-.B ps
-,
-.B fs
-,
-.B ns
-,
-.B us
-,
-.B ms
-or
-.B s
-
-
-.BI "-[no]w" "no "
- View output xvg, xpm, eps and pdb files
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.BI "-type" " enum" " no"
- Compute diffusion coefficient in one direction:
-.B no
-,
-.B x
-,
-.B y
-or
-.B z
-
-
-.BI "-lateral" " enum" " no"
- Calculate the lateral diffusion in a plane perpendicular to:
-.B no
-,
-.B x
-,
-.B y
-or
-.B z
-
-
-.BI "-ngroup" " int" " 1"
- Number of groups to calculate MSD for
-
-.BI "-[no]mw" "yes "
- Mass weighted MSD
-
-.BI "-[no]rmcomm" "no "
- Remove center of mass motion
-
-.BI "-trestart" " time" " 10 "
- Time between restarting points in trajectory (ps)
-
-.BI "-beginfit" " time" " -1 "
- Start time for fitting the MSD (ps), -1 is 10%
-
-.BI "-endfit" " time" " -1 "
- End time for fitting the MSD (ps), -1 is 90%
-
+++ /dev/null
-.TH g_nmeig_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_nmeig_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_nmeig_d\fP
-.BI "-f" " hessian.mtx "
-.BI "-s" " topol.tpr "
-.BI "-of" " eigenfreq.xvg "
-.BI "-ol" " eigenval.xvg "
-.BI "-v" " eigenvec.trr "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-[no]xvgr" ""
-.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 mdrun
-.
-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
-. When mass weighting is used, the generated eigenvectors
-will be scaled back to plain cartesian coordinates before generating the
-output - in this case they will no longer be exactly orthogonal in the
-standard cartesian norm (But in the mass weighted norm they would be).
-.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 xml
-
-.BI "-of" " eigenfreq.xvg"
-.B Output
- xvgr/xmgr file
-
-.BI "-ol" " 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 "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.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" " 50"
- Last eigenvector to write away
-
+++ /dev/null
-.TH g_nmens_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_nmens_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_nmens_d\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 "-nice" " int "
-.BI "-[no]xvgr" ""
-.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 xml
-
-.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 "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.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_nmtraj_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_nmtraj_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_nmtraj_d\fP
-.BI "-s" " topol.tpr "
-.BI "-v" " eigenvec.trr "
-.BI "-o" " nmtraj.xtc "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-eignr" " int "
-.BI "-temp" " real "
-.BI "-amplitude" " real "
-.BI "-nframes" " int "
-.SH DESCRIPTION
-
-.B g_nmtraj
-generates an virtual trajectory from an eigenvector,
-corresponding to a harmonic cartesian oscillation around the average
-structure. The eigenvectors should normally be mass-weighted, but you can
-use non-weighted eigenvectors to generate orthogonal motions.
-The output frames are written as a trajectory file covering an entire period, and
-the first frame is the average structure. If you write the trajectory in (or convert to)
-PDB format you can view it directly in PyMol and also render a photorealistic movie.
-Motion amplitudes are calculated from the eigenvalues and a preset temperature,
-assuming equipartition of the energy over all modes. To make the motion clearly visible
-in PyMol you might want to amplify it by setting an unrealistic high temperature.
-However, be aware that both the linear cartesian displacements and mass weighting will
-lead to serious structure deformation for high amplitudes - this is is simply a limitation
-of the cartesian normal mode model. By default the selected eigenvector is set to 7, since
- the first six normal modes are the translational and rotational degrees of freedom.
-.SH FILES
-.BI "-s" " topol.tpr"
-.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
-
-.BI "-v" " eigenvec.trr"
-.B Input
- Full precision trajectory: trr trj
-
-.BI "-o" " nmtraj.xtc"
-.B Output
- Generic trajectory: xtc trr trj gro g96 pdb
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-eignr" " int" " 7"
- Eigenvector to use (first is 1)
-
-.BI "-temp" " real" " 300 "
- Temperature in Kelvin
-
-.BI "-amplitude" " real" " 0.25 "
- Amplitude for modes with eigenvalue=0
-
-.BI "-nframes" " int" " 30"
- Number of frames to generate
-
+++ /dev/null
-.TH g_order_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_order_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_order_d\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 "-Sg" " sg-ang.xvg "
-.BI "-Sk" " sk-dist.xvg "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-dt" " time "
-.BI "-[no]w" ""
-.BI "-[no]xvgr" ""
-.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.
-
-The tetrahedrality order parameters can be determined
-around an atom. Both angle an distance order parameters are calculated. See
-P.-L. Chau and A.J. Hardwick, Mol. Phys., 93, (1998), 511-518.
-for more details.
-
-
-.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 xml
-
-.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
-
-.BI "-Sg" " sg-ang.xvg"
-.B Output
- xvgr/xmgr file
-
-.BI "-Sk" " sk-dist.xvg"
-.B Output
- xvgr/xmgr file
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- Only use frame when t MOD dt = first time (ps)
-
-.BI "-[no]w" "no "
- View output xvg, xpm, eps and pdb files
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.BI "-d" " enum" " z"
- Direction of the normal on the membrane:
-.B z
-,
-.B x
-or
-.B 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_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_potential_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_potential_d\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 "-nice" " int "
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-dt" " time "
-.BI "-[no]w" ""
-.BI "-[no]xvgr" ""
-.BI "-d" " string "
-.BI "-sl" " int "
-.BI "-cb" " int "
-.BI "-ce" " int "
-.BI "-tz" " real "
-.BI "-[no]spherical" ""
-.BI "-ng" " int "
-.BI "-[no]correct" ""
-.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 xml
-
-.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 "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- Only use frame when t MOD dt = first time (ps)
-
-.BI "-[no]w" "no "
- View output xvg, xpm, eps and pdb files
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.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
-
-.BI "-ng" " int" " 1"
- Number of groups to consider
-
-.BI "-[no]correct" "no "
- Assume net zero charge of groups to improve accuracy
-
-.SH KNOWN PROBLEMS
-\- Discarding slices for integration should not be necessary.
-
+++ /dev/null
-.TH g_rama_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_rama_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_rama_d\fP
-.BI "-f" " traj.xtc "
-.BI "-s" " topol.tpr "
-.BI "-o" " rama.xvg "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-dt" " time "
-.BI "-[no]w" ""
-.BI "-[no]xvgr" ""
-.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 xml
-
-.BI "-o" " rama.xvg"
-.B Output
- xvgr/xmgr file
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- Only use frame when t MOD dt = first time (ps)
-
-.BI "-[no]w" "no "
- View output xvg, xpm, eps and pdb files
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
+++ /dev/null
-.TH g_rdf_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_rdf_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_rdf_d\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 "-[no]h" ""
-.BI "-nice" " int "
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-dt" " time "
-.BI "-[no]w" ""
-.BI "-[no]xvgr" ""
-.BI "-bin" " real "
-.BI "-[no]com" ""
-.BI "-rdf" " enum "
-.BI "-[no]pbc" ""
-.BI "-[no]norm" ""
-.BI "-[no]xy" ""
-.BI "-cut" " real "
-.BI "-ng" " int "
-.BI "-fade" " real "
-.BI "-nlevel" " int "
-.BI "-startq" " real "
-.BI "-endq" " real "
-.BI "-energy" " 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.
-With both methods rdf's can also be calculated around axes parallel
-to the z-axis with option
-.B -xy
-.
-
-
-The option
-.B -rdf
-sets the type of rdf to be computed.
-Default is for atoms or particles, but one can also select center
-of mass or geometry of molecules or residues. In all cases only
-the atoms in the index groups are taken into account.
-For molecules and/or the center of mass option a run input file
-is required.
-Other weighting than COM or COG can currently only be achieved
-by providing a run input file with different masses.
-Option
-.B -com
-also works in conjunction with
-.B -rdf
-.
-
-If a run input file is supplied (
-.B -s
-) and
-.B -rdf
-is set
-to
-.B atom
-, 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,
-i.e. the average number of particles within a distance r.
-
-
-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 xml
-
-.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
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- Only use frame when t MOD dt = first time (ps)
-
-.BI "-[no]w" "no "
- View output xvg, xpm, eps and pdb files
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.BI "-bin" " real" " 0.002 "
- Binwidth (nm)
-
-.BI "-[no]com" "no "
- RDF with respect to the center of mass of first group
-
-.BI "-rdf" " enum" " atom"
- RDF type:
-.B atom
-,
-.B mol_com
-,
-.B mol_cog
-,
-.B res_com
-or
-.B res_cog
-
-
-.BI "-[no]pbc" "yes "
- Use periodic boundary conditions for computing distances. Without PBC the maximum range will be three times the larges box edge.
-
-.BI "-[no]norm" "yes "
- Normalize for volume and density
-
-.BI "-[no]xy" "no "
- Use only the x and y components of the distance
-
-.BI "-cut" " real" " 0 "
- Shortest distance (nm) to be considered
-
-.BI "-ng" " int" " 1"
- Number of secondary groups to compute RDFs around a central group
-
-.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 "-nlevel" " int" " 20"
- Number of different colors in the diffraction image
-
-.BI "-startq" " real" " 0 "
- Starting q (1/nm)
-
-.BI "-endq" " real" " 60 "
- Ending q (1/nm)
-
-.BI "-energy" " real" " 12 "
- Energy of the incoming X-ray (keV)
-
+++ /dev/null
-.TH g_rms_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_rms_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_rms_d\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 "-nice" " int "
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-dt" " time "
-.BI "-tu" " enum "
-.BI "-[no]w" ""
-.BI "-[no]xvgr" ""
-.BI "-what" " enum "
-.BI "-[no]pbc" ""
-.BI "-fit" " enum "
-.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 "-[no]mw" ""
-.BI "-nlevels" " int "
-.BI "-ng" " 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),
-see Maiorov & Crippen, PROTEINS
-.B 22
-, 273 (1995).
-This is selected by
-.B -what
-.
-
-Each structure from a trajectory (
-.B -f
-) is compared to a
-reference structure. 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.
-This is useful as a reference for 'significant' values, see
-Maiorov & Crippen, PROTEINS
-.B 22
-, 273 (1995).
-
-
-Option
-.B -prev
-produces the comparison with a previous frame
-the specified number of frames ago.
-
-
-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
-.
-
-
-Option
-.B -fit
-controls the least-squares fitting of
-the structures on top of each other: complete fit (rotation and
-translation), translation only, or no fitting at all.
-
-
-Option
-.B -mw
-controls whether mass weighting is done or not.
-If you select the option (default) and
-supply a valid tpr file masses will be taken from there,
-otherwise the masses will be deduced from the atommass.dat file in
-the GROMACS library directory. This is fine for proteins but not
-necessarily for other molecules. A default mass of 12.011 amu (Carbon)
-is assigned to unknown atoms. You can check whether this happend by
-turning on the
-.B -debug
-flag and inspecting the log file.
-
-
-With
-.B -f2
-, the 'other structures' are taken from a second
-trajectory, this generates a comparison matrix of one trajectory
-versus the other.
-
-
-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 xml
-
-.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 "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- Only use frame when t MOD dt = first time (ps)
-
-.BI "-tu" " enum" " ps"
- Time unit:
-.B ps
-,
-.B fs
-,
-.B ns
-,
-.B us
-,
-.B ms
-or
-.B s
-
-
-.BI "-[no]w" "no "
- View output xvg, xpm, eps and pdb files
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.BI "-what" " enum" " rmsd"
- Structural difference measure:
-.B rmsd
-,
-.B rho
-or
-.B rhosc
-
-
-.BI "-[no]pbc" "yes "
- PBC check
-
-.BI "-fit" " enum" " rot+trans"
- Fit to reference structure:
-.B rot+trans
-,
-.B translation
-or
-.B none
-
-
-.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 "-[no]mw" "yes "
- Use mass weighting for superposition
-
-.BI "-nlevels" " int" " 80"
- Number of levels in the matrices
-
-.BI "-ng" " int" " 1"
- Number of groups to compute RMS between
-
+++ /dev/null
-.TH g_rmsdist_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_rmsdist_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_rmsdist_d\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 "-nice" " int "
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-dt" " time "
-.BI "-[no]w" ""
-.BI "-[no]xvgr" ""
-.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 xml
-
-.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 "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- Only use frame when t MOD dt = first time (ps)
-
-.BI "-[no]w" "no "
- View output xvg, xpm, eps and pdb files
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.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_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_rmsf_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_rmsf_d\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 "-nice" " int "
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-dt" " time "
-.BI "-[no]w" ""
-.BI "-[no]xvgr" ""
-.BI "-[no]res" ""
-.BI "-[no]aniso" ""
-.BI "-[no]fit" ""
-.SH DESCRIPTION
-g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard
-deviation) of atomic positions
-after (optionally) 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 xml
-
-.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 "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- Only use frame when t MOD dt = first time (ps)
-
-.BI "-[no]w" "no "
- View output xvg, xpm, eps and pdb files
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.BI "-[no]res" "no "
- Calculate averages for each residue
-
-.BI "-[no]aniso" "no "
- Compute anisotropic termperature factors
-
-.BI "-[no]fit" "yes "
- Do a least squares superposition before computing RMSF. Without this you must make sure that the reference structure and the trajectory match.
-
+++ /dev/null
-.TH g_rotacf_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_rotacf_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_rotacf_d\fP
-.BI "-f" " traj.xtc "
-.BI "-s" " topol.tpr "
-.BI "-n" " index.ndx "
-.BI "-o" " rotacf.xvg "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-dt" " time "
-.BI "-[no]w" ""
-.BI "-[no]xvgr" ""
-.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 xml
-
-.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 "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- Only use frame when t MOD dt = first time (ps)
-
-.BI "-[no]w" "no "
- View output xvg, xpm, eps and pdb files
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.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):
-.B 0
-,
-.B 1
-,
-.B 2
-or
-.B 3
-
-
-.BI "-fitfn" " enum" " none"
- Fit function:
-.B none
-,
-.B exp
-,
-.B aexp
-,
-.B exp_exp
-,
-.B vac
-,
-.B exp5
-,
-.B exp7
-or
-.B exp9
-
-
-.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_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_saltbr_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_saltbr_d\fP
-.BI "-f" " traj.xtc "
-.BI "-s" " topol.tpr "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-dt" " time "
-.BI "-t" " real "
-.BI "-[no]sep" ""
-.SH DESCRIPTION
-g_saltbr plots the distance 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, plus-min.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 xml
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- 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_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_sas_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_sas_d\fP
-.BI "-f" " traj.xtc "
-.BI "-s" " topol.tpr "
-.BI "-o" " area.xvg "
-.BI "-or" " resarea.xvg "
-.BI "-oa" " atomarea.xvg "
-.BI "-tv" " volume.xvg "
-.BI "-q" " connelly.pdb "
-.BI "-n" " index.ndx "
-.BI "-i" " surfat.itp "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-dt" " time "
-.BI "-[no]w" ""
-.BI "-[no]xvgr" ""
-.BI "-probe" " real "
-.BI "-ndots" " int "
-.BI "-qmax" " real "
-.BI "-[no]f_index" ""
-.BI "-minarea" " real "
-.BI "-[no]pbc" ""
-.BI "-[no]prot" ""
-.BI "-dgs" " real "
-.SH DESCRIPTION
-g_sas computes hydrophobic, hydrophilic 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 program will ask for a group for the surface calculation
-and a group for the output. The calculation group should always
-consists of all the non-solvent atoms in the system.
-The output group can be the whole or part of the calculation group.
-The area can be plotted
-per residue and atom as well (options
-.B -or
-and
-.B -oa
-).
-In combination with the latter option an
-.B itp
-file can be
-generated (option
-.B -i
-)
-which can be used to restrain surface atoms.
-
-
-By default, periodic boundary conditions are taken into account,
-this can be turned off using the
-.B -pbc
-option.
-
-
-With the
-.B -tv
-option the total volume and density of the molecule can be
-computed.
-Please consider whether the normal probe radius is appropriate
-in this case or whether you would rather use e.g. 0. It is good
-to keep in mind that the results for volume and density are very
-approximate, in e.g. ice Ih one can easily fit water molecules in the
-pores which would yield too low volume, too high surface area and too
-high density.
-.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 xml
-
-.BI "-o" " area.xvg"
-.B Output
- xvgr/xmgr file
-
-.BI "-or" " resarea.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.BI "-oa" " atomarea.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.BI "-tv" " volume.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.BI "-q" " connelly.pdb"
-.B Output, Opt.
- Protein data bank 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 "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- Only use frame when t MOD dt = first time (ps)
-
-.BI "-[no]w" "no "
- View output xvg, xpm, eps and pdb files
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.BI "-probe" " 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 "-[no]f_index" "no "
- Determine from a group in the index file what are the hydrophobic atoms rather than from the charge
-
-.BI "-minarea" " real" " 0.5 "
- The minimum area (nm2) to count an atom as a surface atom when writing a position restraint file (see help)
-
-.BI "-[no]pbc" "yes "
- Take periodicity into account
-
-.BI "-[no]prot" "yes "
- Output the protein to the connelly pdb file too
-
-.BI "-dgs" " real" " 0 "
- default value for solvation free energy per area (kJ/mol/nm2)
-
+++ /dev/null
-.TH g_sdf_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_sdf_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_sdf_d\fP
-.BI "-f" " traj.xtc "
-.BI "-n" " index.ndx "
-.BI "-s" " topol.tpr "
-.BI "-o" " gom_plt.dat "
-.BI "-r" " refmol.gro "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-dt" " time "
-.BI "-mode" " int "
-.BI "-triangle" " vector "
-.BI "-dtri" " vector "
-.BI "-bin" " real "
-.BI "-grid" " vector "
-.SH DESCRIPTION
-g_sdf calculates the spatial distribution function (SDF) of a set of atoms
-within a coordinate system defined by three atoms. There is single body,
-two body and three body SDF implemented (select with option -mode).
-In the single body case the local coordinate system is defined by using
-a triple of atoms from one single molecule, for the two and three body case
-the configurations are dynamically searched complexes of two or three
-molecules (or residues) meeting certain distance consitions (see below).
-
-
-The program needs a trajectory, a GROMACS run input file and an index
-file to work.
-You have to setup 4 groups in the index file before using g_sdf:
-
-
-The first three groups are used to define the SDF coordinate system.
-The programm will dynamically generate the atom tripels according to
-the selected -mode:
-In -mode 1 the triples will be just the 1st, 2nd, 3rd, ... atoms from
-groups 1, 2 and 3. Hence the nth entries in groups 1, 2 and 3 must be from the
-same residue. In -mode 2 the triples will be 1st, 2nd, 3rd, ... atoms from
-groups 1 and 2 (with the nth entries in groups 1 and 2 having the same res-id).
-For each pair from groups 1 and 2 group 3 is searched for an atom meeting the
-distance conditions set with -triangle and -dtri relative to atoms 1 and 2. In
--mode 3 for each atom in group 1 group 2 is searched for an atom meeting the
-distance condition and if a pair is found group 3 is searched for an atom
-meeting the further conditions. The triple will only be used if all three atoms
-have different res-id's.
-
-
-The local coordinate system is always defined using the following scheme:
-Atom 1 will be used as the point of origin for the SDF. Atom 1 and 2 will define the principle axis (Z) of the coordinate system.
-The other two axis will be defined inplane (Y) and normal (X) to the plane through
-Atoms 1, 2 and 3. The fourth group
-contains the atoms for which the SDF will be evaluated.
-
-
-For -mode 2 and 3 you have to define the distance conditions for the
-2 resp. 3 molecule complexes to be searched for using -triangle and -dtri.
-
-
-The SDF will be sampled in cartesian coordinates.
-Use '-grid x y z' to define the size of the SDF grid around the
-reference molecule.
-The Volume of the SDF grid will be V=x*y*z (nm3). Use -bin to set the binwidth for grid.
-
-
-The output will be a binary 3D-grid file (gom_plt.dat) in the .plt format that can be be
-read directly by gOpenMol.
-The option -r will generate a .gro file with the reference molecule(s) transfered to
-the SDF coordinate system. Load this file into gOpenMol and display the
-SDF as a contour plot (see http://www.csc.fi/gopenmol/index.phtml for
-further documentation).
-
-
-For further information about SDF's have a look at: A. Vishnyakov, JPC A, 105,
-2001, 1702 and the references cited within.
-.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, Opt.
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
-
-.BI "-o" " gom_plt.dat"
-.B Output
- Generic data file
-
-.BI "-r" " refmol.gro"
-.B Output, Opt.
- Generic structure: gro g96 pdb xml
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- Only use frame when t MOD dt = first time (ps)
-
-.BI "-mode" " int" " 1"
- SDF in [1,2,3] particle mode
-
-.BI "-triangle" " vector" " 0 0 0"
- r(1,3), r(2,3), r(1,2)
-
-.BI "-dtri" " vector" " 0.03 0.03 0.03"
- dr(1,3), dr(2,3), dr(1,2)
-
-.BI "-bin" " real" " 0.05 "
- Binwidth for the 3D-grid (nm)
-
-.BI "-grid" " vector" " 1 1 1"
- Size of the 3D-grid (nm,nm,nm)
-
+++ /dev/null
-.TH g_sgangle_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_sgangle_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_sgangle_d\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 "-nice" " int "
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-dt" " time "
-.BI "-[no]w" ""
-.BI "-[no]xvgr" ""
-.BI "-[no]pbc" ""
-.BI "-[no]one" ""
-.BI "-[no]z" ""
-.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.
-If -one is set, only one group should be specified in the index
-file and the angle between this group at time 0 and t will be computed.
-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 xml
-
-.BI "-oa" " sg_angle.xvg"
-.B Output
- xvgr/xmgr file
-
-.BI "-od" " sg_dist.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.BI "-od1" " sg_dist1.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.BI "-od2" " sg_dist2.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- Only use frame when t MOD dt = first time (ps)
-
-.BI "-[no]w" "no "
- View output xvg, xpm, eps and pdb files
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.BI "-[no]pbc" "no "
- Use periodic boundary conditions
-
-.BI "-[no]one" "no "
- Only one group compute angle between vector at time zero and time t
-
-.BI "-[no]z" "no "
- Use the Z-axis as reference
-
+++ /dev/null
-.TH g_sham_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_sham_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_sham_d\fP
-.BI "-f" " graph.xvg "
-.BI "-ge" " gibbs.xvg "
-.BI "-ene" " esham.xvg "
-.BI "-dist" " ener.xvg "
-.BI "-histo" " edist.xvg "
-.BI "-bin" " bindex.ndx "
-.BI "-ls" " gibbs.xpm "
-.BI "-lsh" " enthalpy.xpm "
-.BI "-lss" " entropy.xpm "
-.BI "-map" " map.xpm "
-.BI "-ls3" " gibbs3.pdb "
-.BI "-mdata" " mapdata.xvg "
-.BI "-g" " shamlog.log "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-[no]w" ""
-.BI "-[no]xvgr" ""
-.BI "-[no]time" ""
-.BI "-b" " real "
-.BI "-e" " real "
-.BI "-ttol" " real "
-.BI "-n" " int "
-.BI "-[no]d" ""
-.BI "-bw" " real "
-.BI "-[no]sham" ""
-.BI "-tsham" " real "
-.BI "-pmin" " real "
-.BI "-dim" " vector "
-.BI "-ngrid" " vector "
-.BI "-xmin" " vector "
-.BI "-xmax" " vector "
-.BI "-gmax" " real "
-.BI "-emin" " real "
-.BI "-emax" " real "
-.BI "-nlevels" " int "
-.BI "-mname" " string "
-.SH DESCRIPTION
-g_sham makes multi-dimensional free-energy, enthalpy and entropy plots.
-g_sham reads one or more xvg files and analyzes data sets.
-g_sham basic purpose is plotting Gibbs free energy landscapes
-by Bolzmann inverting multi-dimensional histograms, but it can also
-make enthalpy (option
-.B -lsh
-) and entropy (option
-.B -lss
-)
-plots. The histograms can be made for any quantities the user supplies.
-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.
-
-
-
-Option
-.B -ge
-can be used to supply a file with free energies
-when the ensemble is not a Boltzmann ensemble, but needs to be biased
-by this free energy. One free energy value is required for each
-(multi-dimensional) data point in the
-.B -f
-input.
-
-
-
-Option
-.B -ene
-can be used to supply a file with energies.
-These energies are used as a weighting function in the single
-histogram analysis method due to Kumar et. al. When also temperatures
-are supplied (as a second column in the file) an experimental
-weighting scheme is applied. In addition the vales
-are used for making enthalpy and entropy plots.
-
-
-
-With option
-.B -dim
-dimensions can be gives for distances.
-When a distance is 2- or 3-dimensional, the circumference or surface
-sampled by two particles increases with increasing distance.
-Depending on what one would like to show, one can choose to correct
-the free-energy for this volume effect.
-The probability is normalized by r and r2 for a dimension of 2 and 3
-respectively.
-A value of -1 is used to indicate an angle in degrees between two
-vectors: a sin(angle) normalization will be applied.
-Note that for angles between vectors the inner-product or cosine
-is the natural quantity to use, as it will produce bins of the same
-volume.
-.SH FILES
-.BI "-f" " graph.xvg"
-.B Input
- xvgr/xmgr file
-
-.BI "-ge" " gibbs.xvg"
-.B Input, Opt.
- xvgr/xmgr file
-
-.BI "-ene" " esham.xvg"
-.B Input, Opt.
- xvgr/xmgr file
-
-.BI "-dist" " ener.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.BI "-histo" " edist.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.BI "-bin" " bindex.ndx"
-.B Output, Opt.
- Index file
-
-.BI "-ls" " gibbs.xpm"
-.B Output, Opt.
- X PixMap compatible matrix file
-
-.BI "-lsh" " enthalpy.xpm"
-.B Output, Opt.
- X PixMap compatible matrix file
-
-.BI "-lss" " entropy.xpm"
-.B Output, Opt.
- X PixMap compatible matrix file
-
-.BI "-map" " map.xpm"
-.B Output, Opt.
- X PixMap compatible matrix file
-
-.BI "-ls3" " gibbs3.pdb"
-.B Output, Opt.
- Protein data bank file
-
-.BI "-mdata" " mapdata.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.BI "-g" " shamlog.log"
-.B Output, Opt.
- Log file
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-[no]w" "no "
- View output xvg, xpm, eps and pdb files
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.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 "-ttol" " real" " 0 "
- Tolerance on time in appropriate units (usually ps)
-
-.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 "-[no]sham" "yes "
- Turn off energy weighting even if energies are given
-
-.BI "-tsham" " real" " 298.15"
- Temperature for single histogram analysis
-
-.BI "-pmin" " real" " 0 "
- Minimum probability. Anything lower than this will be set to zero
-
-.BI "-dim" " vector" " 1 1 1"
- Dimensions for distances, used for volume correction (max 3 values, dimensions 3 will get the same value as the last)
-
-.BI "-ngrid" " vector" " 32 32 32"
- Number of bins for energy landscapes (max 3 values, dimensions 3 will get the same value as the last)
-
-.BI "-xmin" " vector" " 0 0 0"
- Minimum for the axes in energy landscape (see above for 3 dimensions)
-
-.BI "-xmax" " vector" " 1 1 1"
- Maximum for the axes in energy landscape (see above for 3 dimensions)
-
-.BI "-gmax" " real" " 0 "
- Maximum free energy in output, default is calculate
-
-.BI "-emin" " real" " 0 "
- Minimum enthalpy in output, default is calculate
-
-.BI "-emax" " real" " 0 "
- Maximum enthalpy in output, default is calculate
-
-.BI "-nlevels" " int" " 25"
- Number of levels for energy landscape
-
-.BI "-mname" " string" " "
- Legend label for the custom landscape
-
+++ /dev/null
-.TH g_sorient_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_sorient_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_sorient_d\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 "-rc" " scount.xvg "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-dt" " time "
-.BI "-[no]w" ""
-.BI "-[no]xvgr" ""
-.BI "-[no]com" ""
-.BI "-[no]v23" ""
-.BI "-rmin" " real "
-.BI "-rmax" " real "
-.BI "-cbin" " real "
-.BI "-rbin" " real "
-.BI "-[no]pbc" ""
-.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, or when the option
-.B -v23
-is set
-the angle with the vector between atoms 2 and 3.
-
-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 for
-.B -o
-and
-.B -no
-each frame.
-
-
-
-.B -o
-: distribtion of cos(theta1) for rmin=r=rmax.
-
-
-
-.B -no
-: distribution of cos(theta2) for rmin=r=rmax.
-
-
-
-.B -ro
-: cos(theta1) and 3cos2(theta2)-1 as a function of the
-distance.
-
-
-
-.B -co
-: the sum over all solvent molecules within distance r
-of cos(theta1) and 3cos2(theta2)-1 as a function of r.
-
-
-
-.B -rc
-: the distribution of the solvent molecules 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 xml
-
-.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
-
-.BI "-rc" " scount.xvg"
-.B Output
- xvgr/xmgr file
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- Only use frame when t MOD dt = first time (ps)
-
-.BI "-[no]w" "no "
- View output xvg, xpm, eps and pdb files
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.BI "-[no]com" "no "
- Use the center of mass as the reference postion
-
-.BI "-[no]v23" "no "
- Use the vector between atoms 2 and 3
-
-.BI "-rmin" " real" " 0 "
- Minimum distance (nm)
-
-.BI "-rmax" " real" " 0.5 "
- Maximum distance (nm)
-
-.BI "-cbin" " real" " 0.02 "
- Binwidth for the cosine
-
-.BI "-rbin" " real" " 0.02 "
- Binwidth for r (nm)
-
-.BI "-[no]pbc" "no "
- Check PBC for the center of mass calculation. Only necessary when your reference group consists of several molecules.
-
+++ /dev/null
-.TH g_spatial_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_spatial_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_spatial_d\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 "-nice" " int "
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-dt" " time "
-.BI "-tu" " enum "
-.BI "-[no]w" ""
-.BI "-[no]xvgr" ""
-.BI "-[no]dista" ""
-.BI "-nlevels" " int "
-.BI "-cutoff" " real "
-.BI "-[no]fit" ""
-.BI "-max" " real "
-.BI "-skip" " int "
-.BI "-[no]av" ""
-.BI "-wcl" " int "
-.BI "-nst" " int "
-.BI "-rmsmin" " real "
-.BI "-method" " enum "
-.BI "-minstruct" " int "
-.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.
-
-
-single 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 (single 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.
-
-Two output files are always written:
-
-
-.B -o
-writes the RMSD values in the upper left half of the matrix
-and a graphical depiction of the clusters in the lower right half
-When
-.B -minstruct
-= 1 the graphical depiction is black
-when two structures are in the same cluster.
-When
-.B -minstruct
- 1 different colors will be used for each
-cluster.
-
-
-.B -g
-writes information on the options used and a detailed list
-of all clusters and their members.
-
-
-Additionally, a number of optional output files can be written:
-
-
-.B -dist
-writes the RMSD distribution.
-
-
-.B -ev
-writes the eigenvectors of the RMSD matrix
-diagonalization.
-
-
-.B -sz
-writes the cluster sizes.
-
-
-.B -tr
-writes a matrix of the number transitions between
-cluster pairs.
-
-
-.B -ntr
-writes the total number of transitions to or from
-each cluster.
-
-
-.B -clid
-writes the cluster number as a function of time.
-
-
-.B -cl
-writes average (with option
-.B -av
-) or central
-structure of each cluster or writes numbered files with cluster members
-for a selected set of clusters (with option
-.B -wcl
-, depends on
-
-.B -nst
-and
-.B -rmsmin
-).
-
-.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 xml
-
-.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 "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- Only use frame when t MOD dt = first time (ps)
-
-.BI "-tu" " enum" " ps"
- Time unit:
-.B ps
-,
-.B fs
-,
-.B ns
-,
-.B us
-,
-.B ms
-or
-.B s
-
-
-.BI "-[no]w" "no "
- View output xvg, xpm, eps and pdb files
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.BI "-[no]dista" "no "
- Use RMSD of distances instead of RMS deviation
-
-.BI "-nlevels" " int" " 40"
- Discretize RMSD matrix in levels
-
-.BI "-cutoff" " real" " 0.1 "
- RMSD cut-off (nm) for two structures to be neighbor
-
-.BI "-[no]fit" "yes "
- Use least squares fitting before RMSD calculation
-
-.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:
-.B linkage
-,
-.B jarvis-patrick
-,
-.B monte-carlo
-,
-.B diagonalization
-or
-.B gromos
-
-
-.BI "-minstruct" " int" " 1"
- Minimum number of structures in cluster for coloring in the xpm file
-
-.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_spol_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_spol_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_spol_d\fP
-.BI "-f" " traj.xtc "
-.BI "-s" " topol.tpr "
-.BI "-n" " index.ndx "
-.BI "-o" " scdist.xvg "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-dt" " time "
-.BI "-[no]w" ""
-.BI "-[no]xvgr" ""
-.BI "-[no]com" ""
-.BI "-[no]pbc" ""
-.BI "-refat" " int "
-.BI "-rmin" " real "
-.BI "-rmax" " real "
-.BI "-dip" " real "
-.BI "-bw" " real "
-.SH DESCRIPTION
-g_spol analyzes dipoles around a solute; it is especially useful
-for polarizable water. A group of reference atoms, or a center
-of mass reference (option
-.B -com
-) and a group of solvent
-atoms is required. The program splits the group of solvent atoms
-into molecules. For each solvent molecule the distance to the
-closest atom in reference group or to the COM is determined.
-A cumulative distribution of these distances is plotted.
-For each distance between
-.B -rmin
-and
-.B -rmax
-
-the inner product of the distance vector
-and the dipole of the solvent molecule is determined.
-The average of these dipole components is printed.
-The same is done for the polarization, where the average dipole is
-subtracted from the instantaneous dipole. The magnitude of the average
-dipole is set with the option
-.B -dip
-, the direction is defined
-by the vector from the first atom in the selected solvent group
-to the midpoint between the second and the third atom.
-.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 xml
-
-.BI "-n" " index.ndx"
-.B Input, Opt.
- Index file
-
-.BI "-o" " scdist.xvg"
-.B Output
- xvgr/xmgr file
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- Only use frame when t MOD dt = first time (ps)
-
-.BI "-[no]w" "no "
- View output xvg, xpm, eps and pdb files
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.BI "-[no]com" "no "
- Use the center of mass as the reference postion
-
-.BI "-[no]pbc" "no "
- Check PBC for the center of mass calculation. Only necessary when your reference group consists of several molecules.
-
-.BI "-refat" " int" " 1"
- The reference atom of the solvent molecule
-
-.BI "-rmin" " real" " 0 "
- Maximum distance (nm)
-
-.BI "-rmax" " real" " 0.32 "
- Maximum distance (nm)
-
-.BI "-dip" " real" " 0 "
- The average dipole (D)
-
-.BI "-bw" " real" " 0.01 "
- The bin width
-
+++ /dev/null
-.TH g_tcaf_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_tcaf_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_tcaf_d\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 "-nice" " int "
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-dt" " time "
-.BI "-[no]w" ""
-.BI "-[no]xvgr" ""
-.BI "-[no]mol" ""
-.BI "-[no]k34" ""
-.BI "-wt" " 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_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 xml
-
-.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 "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- Only use frame when t MOD dt = first time (ps)
-
-.BI "-[no]w" "no "
- View output xvg, xpm, eps and pdb files
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.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
-
-.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):
-.B 0
-,
-.B 1
-,
-.B 2
-or
-.B 3
-
-
-.BI "-fitfn" " enum" " none"
- Fit function:
-.B none
-,
-.B exp
-,
-.B aexp
-,
-.B exp_exp
-,
-.B vac
-,
-.B exp5
-,
-.B exp7
-or
-.B exp9
-
-
-.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_traj_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_traj_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_traj_d\fP
-.BI "-f" " traj.xtc "
-.BI "-s" " topol.tpr "
-.BI "-n" " index.ndx "
-.BI "-ox" " coord.xvg "
-.BI "-oxt" " coord.xtc "
-.BI "-ov" " veloc.xvg "
-.BI "-of" " force.xvg "
-.BI "-ob" " box.xvg "
-.BI "-ot" " temp.xvg "
-.BI "-ekt" " ektrans.xvg "
-.BI "-ekr" " ekrot.xvg "
-.BI "-vd" " veldist.xvg "
-.BI "-cv" " veloc.pdb "
-.BI "-cf" " force.pdb "
-.BI "-av" " all_veloc.xvg "
-.BI "-af" " all_force.xvg "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-dt" " time "
-.BI "-tu" " enum "
-.BI "-[no]w" ""
-.BI "-[no]xvgr" ""
-.BI "-[no]com" ""
-.BI "-[no]mol" ""
-.BI "-[no]nojump" ""
-.BI "-[no]x" ""
-.BI "-[no]y" ""
-.BI "-[no]z" ""
-.BI "-ng" " int "
-.BI "-[no]len" ""
-.BI "-bin" " real "
-.BI "-scale" " real "
-.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,
-provided velocities are present in the trajectory file.
-No corrections are made for constrained degrees of freedom!
-This implies
-.B -com
-.
-
-
-Options
-.B -ekt
-and
-.B -ekr
-plot the translational and
-rotational kinetic energy of each group,
-provided velocities are present in the trajectory file.
-This implies
-.B -com
-.
-
-
-Options
-.B -cv
-and
-.B -cf
-write the average velocities
-and average forces as temperature factors to a pdb file with
-the average coordinates. The temperature factors are scaled such
-that the maximum is 10. The scaling can be changed with the option
-
-.B -scale
-. To get the velocities or forces of one
-frame set both
-.B -b
-and
-.B -e
-to the time of
-desired frame. When averaging over frames you might need to use
-the
-.B -nojump
-option to obtain the correct average coordinates.
-If you select either of these option the average force and velocity
-for each atom are written to an xvg file as well
-(specified with
-.B -av
-or
-.B -af
-).
-
-
-Option
-.B -vd
-computes a velocity distribution, i.e. the
-norm of the vector is plotted. In addition in the same graph
-the kinetic energy distribution is given.
-.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 xml
-
-.BI "-n" " index.ndx"
-.B Input, Opt.
- Index file
-
-.BI "-ox" " coord.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.BI "-oxt" " coord.xtc"
-.B Output, Opt.
- Generic trajectory: xtc trr trj gro g96 pdb
-
-.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 "-ekt" " ektrans.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.BI "-ekr" " ekrot.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.BI "-vd" " veldist.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.BI "-cv" " veloc.pdb"
-.B Output, Opt.
- Protein data bank file
-
-.BI "-cf" " force.pdb"
-.B Output, Opt.
- Protein data bank file
-
-.BI "-av" " all_veloc.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.BI "-af" " all_force.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- Only use frame when t MOD dt = first time (ps)
-
-.BI "-tu" " enum" " ps"
- Time unit:
-.B ps
-,
-.B fs
-,
-.B ns
-,
-.B us
-,
-.B ms
-or
-.B s
-
-
-.BI "-[no]w" "no "
- View output xvg, xpm, eps and pdb files
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.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 "-ng" " int" " 1"
- Number of groups to consider
-
-.BI "-[no]len" "no "
- Plot vector length
-
-.BI "-bin" " real" " 1 "
- Binwidth for velocity histogram (nm/ps)
-
-.BI "-scale" " real" " 0 "
- Scale factor for pdb output, 0 is autoscale
-
+++ /dev/null
-.TH g_vanhove_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_vanhove_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_vanhove_d\fP
-.BI "-f" " traj.xtc "
-.BI "-s" " topol.tpr "
-.BI "-n" " index.ndx "
-.BI "-om" " vanhove.xpm "
-.BI "-or" " vanhove_r.xvg "
-.BI "-ot" " vanhove_t.xvg "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-dt" " time "
-.BI "-[no]w" ""
-.BI "-[no]xvgr" ""
-.BI "-sqrt" " real "
-.BI "-fm" " int "
-.BI "-rmax" " real "
-.BI "-rbin" " real "
-.BI "-mmax" " real "
-.BI "-nlevels" " int "
-.BI "-nr" " int "
-.BI "-fr" " int "
-.BI "-rt" " real "
-.BI "-ft" " int "
-.SH DESCRIPTION
-g_vanhove computes the Van Hove correlation function.
-The Van Hove G(r,t) is the probability that a particle that is at r0
-at time zero can be found at position r0+r at time t.
-g_vanhove determines G not for a vector r, but for the length of r.
-Thus it gives the probability that a particle moves a distance of r
-in time t.
-Jumps across the periodic boundaries are removed.
-Corrections are made for scaling due to isotropic
-or anisotropic pressure coupling.
-
-
-
-With option
-.B -om
-the whole matrix can be written as a function
-of t and r or as a function of sqrt(t) and r (option
-.B -sqrt
-).
-
-
-
-With option
-.B -or
-the Van Hove function is plotted for one
-or more values of t. Option
-.B -nr
-sets the number of times,
-option
-.B -fr
-the number spacing between the times.
-The binwidth is set with option
-.B -rbin
-. The number of bins
-is determined automatically.
-
-
-
-With option
-.B -ot
-the integral up to a certain distance
-(option
-.B -rt
-) is plotted as a function of time.
-
-
-
-For all frames that are read the coordinates of the selected particles
-are stored in memory. Therefore the program may use a lot of memory.
-For options
-.B -om
-and
-.B -ot
-the program may be slow.
-This is because the calculation scales as the number of frames times
-
-.B -fm
-or
-.B -ft
-.
-Note that with the
-.B -dt
-option the memory usage and calculation
-time can be reduced.
-.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 xml
-
-.BI "-n" " index.ndx"
-.B Input, Opt.
- Index file
-
-.BI "-om" " vanhove.xpm"
-.B Output, Opt.
- X PixMap compatible matrix file
-
-.BI "-or" " vanhove_r.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.BI "-ot" " vanhove_t.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- Only use frame when t MOD dt = first time (ps)
-
-.BI "-[no]w" "no "
- View output xvg, xpm, eps and pdb files
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.BI "-sqrt" " real" " 0 "
- Use sqrt(t) on the matrix axis which binspacing in sqrt(ps)
-
-.BI "-fm" " int" " 0"
- Number of frames in the matrix, 0 is plot all
-
-.BI "-rmax" " real" " 2 "
- Maximum r in the matrix (nm)
-
-.BI "-rbin" " real" " 0.01 "
- Binwidth in the matrix and for -or (nm)
-
-.BI "-mmax" " real" " 0 "
- Maximum density in the matrix, 0 is calculate (1/nm)
-
-.BI "-nlevels" " int" " 81"
- Number of levels in the matrix
-
-.BI "-nr" " int" " 1"
- Number of curves for the -or output
-
-.BI "-fr" " int" " 0"
- Frame spacing for the -or output
-
-.BI "-rt" " real" " 0 "
- Integration limit for the -ot output (nm)
-
-.BI "-ft" " int" " 0"
- Number of frames in the -ot output, 0 is plot all
-
+++ /dev/null
-.TH g_velacc_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_velacc_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_velacc_d\fP
-.BI "-f" " traj.trr "
-.BI "-s" " topol.tpr "
-.BI "-n" " index.ndx "
-.BI "-o" " vac.xvg "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-dt" " time "
-.BI "-[no]w" ""
-.BI "-[no]xvgr" ""
-.BI "-[no]m" ""
-.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 -m
-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 xml
-
-.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 "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- Only use frame when t MOD dt = first time (ps)
-
-.BI "-[no]w" "no "
- View output xvg, xpm, eps and pdb files
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.BI "-[no]m" "no "
- Calculate the momentum autocorrelation function
-
-.BI "-[no]mol" "no "
- Calculate the momentum acf 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):
-.B 0
-,
-.B 1
-,
-.B 2
-or
-.B 3
-
-
-.BI "-fitfn" " enum" " none"
- Fit function:
-.B none
-,
-.B exp
-,
-.B aexp
-,
-.B exp_exp
-,
-.B vac
-,
-.B exp5
-,
-.B exp7
-or
-.B exp9
-
-
-.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_wham_d 1 "Thu 16 Oct 2008"
-.SH NAME
-g_wham_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3g_wham_d\fP
-.BI "-o" " profile.xvg "
-.BI "-hist" " histo.xvg "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-[no]w" ""
-.BI "-[no]xvgr" ""
-.BI "-min" " real "
-.BI "-max" " real "
-.BI "-bins" " int "
-.BI "-[no]prof" ""
-.BI "-temp" " real "
-.BI "-[no]flip" ""
-.BI "-tol" " real "
-.SH DESCRIPTION
-This is an analysis program that implements the Weighted
-Histogram Analysis Method (WHAM). It is intended to analyze
-.pdo files generated by mdrun using umbrella sampling tocreate a potential of mean force (PMF). The options are
-
-
-.B -o
- name of the PMF output file
-
-
-.B -hist
- name of the histograms output file
-
-
-.B -min
- minimum coordinate to use
-
-
-.B -max
- maximum coordinate to use
-
-
-Note: the program will throw out any data that is outside
-of min - max. The program will output the true min and max
-after completion, so you can use these values the next time.
-or you can use:
-
-
-.B -noprof
-only calculate min and max
-
-
-.B -bins
- number of bins to use in calculation
-
-.SH FILES
-.BI "-o" " profile.xvg"
-.B Output
- xvgr/xmgr file
-
-.BI "-hist" " histo.xvg"
-.B Output
- xvgr/xmgr file
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 0"
- Set the nicelevel
-
-.BI "-[no]w" "no "
- View output xvg, xpm, eps and pdb files
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.BI "-min" " real" " 1.99916e+37"
- Minimum coordinate in profile
-
-.BI "-max" " real" " 0 "
- Maximum coordinate in profile
-
-.BI "-bins" " int" " 100"
- Number of bins in profile
-
-.BI "-[no]prof" "yes "
- Only calculate min and max
-
-.BI "-temp" " real" " 2.68219e-314"
- Temperature
-
-.BI "-[no]flip" "no "
- Combine halves of profile
-
-.BI "-tol" " real" " 0.01 "
- Tolerance
-
+++ /dev/null
-.TH genbox_d 1 "Thu 16 Oct 2008"
-.SH NAME
-genbox_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3genbox_d\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 "-nice" " int "
-.BI "-box" " vector "
-.BI "-nmol" " int "
-.BI "-try" " int "
-.BI "-seed" " int "
-.BI "-vdwd" " real "
-.BI "-shell" " real "
-.BI "-maxsol" " int "
-.BI "-[no]vel" ""
-.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), with coordinates
-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 xml
-
-.BI "-cs" " spc216.gro"
-.B Input, Opt., Lib.
- Generic structure: gro g96 pdb tpr tpb tpa xml
-
-.BI "-ci" " insert.gro"
-.B Input, Opt.
- Generic structure: gro g96 pdb tpr tpb tpa xml
-
-.BI "-o" " out.gro"
-.B Output
- Generic structure: gro g96 pdb xml
-
-.BI "-p" " topol.top"
-.B In/Out, Opt.
- Topology file
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.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
-
-.BI "-maxsol" " int" " 0"
- maximum number of solvent molecules to add if they fit in the box. If zero (default) this is ignored
-
-.BI "-[no]vel" "no "
- keep velocities from input solute and solvent
-
-.SH KNOWN PROBLEMS
-\- Molecules must be whole in the initial configurations.
-
+++ /dev/null
-.TH genconf_d 1 "Thu 16 Oct 2008"
-.SH NAME
-genconf_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3genconf_d\fP
-.BI "-f" " conf.gro "
-.BI "-o" " out.gro "
-.BI "-trj" " traj.xtc "
-.BI "-[no]h" ""
-.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 xml
-
-.BI "-o" " out.gro"
-.B Output
- Generic structure: gro g96 pdb xml
-
-.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 "-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" "yes "
- Renumber residues
-
-.SH KNOWN PROBLEMS
-\- The program should allow for random displacement off lattice points.
-
+++ /dev/null
-.TH genion_d 1 "Thu 16 Oct 2008"
-.SH NAME
-genion_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3genion_d\fP
-.BI "-s" " topol.tpr "
-.BI "-table" " table.xvg "
-.BI "-n" " index.ndx "
-.BI "-o" " out.gro "
-.BI "-g" " genion.log "
-.BI "-pot" " pot.pdb "
-.BI "-p" " topol.top "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-[no]xvgr" ""
-.BI "-np" " int "
-.BI "-pname" " string "
-.BI "-pq" " int "
-.BI "-nn" " int "
-.BI "-nname" " string "
-.BI "-nq" " int "
-.BI "-rmin" " real "
-.BI "-[no]random" ""
-.BI "-seed" " int "
-.BI "-scale" " real "
-.BI "-conc" " real "
-.BI "-[no]neutral" ""
-.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, shift function
-or user function can be used. For the user function a table file
-can be specified with the option
-.B -table
-.
-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.
-
-
-With the option
-.B -pot
-the potential can be written as B-factors
-in a pdb file (for visualisation using e.g. rasmol).
-The unit of the potential is 1000 kJ/(mol e), the scaling be changed
-with the
-.B -scale
-option.
-
-
-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 xml
-
-.BI "-table" " table.xvg"
-.B Input, Opt.
- xvgr/xmgr file
-
-.BI "-n" " index.ndx"
-.B Input, Opt.
- Index file
-
-.BI "-o" " out.gro"
-.B Output
- Generic structure: gro g96 pdb xml
-
-.BI "-g" " genion.log"
-.B Output
- Log file
-
-.BI "-pot" " pot.pdb"
-.B Output, Opt.
- Protein data bank file
-
-.BI "-p" " topol.top"
-.B In/Out, Opt.
- Topology file
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.BI "-np" " int" " 0"
- Number of positive ions
-
-.BI "-pname" " string" " Na"
- Name of the positive ion
-
-.BI "-pq" " int" " 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" " int" " -1"
- Charge of the negative ion
-
-.BI "-rmin" " real" " 0.6 "
- Minimum distance between ions
-
-.BI "-[no]random" "yes "
- 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
-
-.BI "-scale" " real" " 0.001 "
- Scaling factor for the potential for -pot
-
-.BI "-conc" " real" " 0 "
- Specify salt concentration (mol/liter). This will add sufficient ions to reach up to the specified concentration as computed from the volume of the cell in the input tpr file. Overrides the -np and nn options.
-
-.BI "-[no]neutral" "no "
- This option will add enough ions to neutralize the system. In combination with the concentration option a neutral system at a given salt concentration will be generated.
-
-.SH KNOWN PROBLEMS
-\- Calculation of the potential is not reliable, therefore the
-.B -random
-option is now turned on by default.
-
-\- If you specify a salt concentration existing ions are not taken into account. In effect you therefore specify the amount of salt to be added.
-
+++ /dev/null
-.TH genrestr_d 1 "Thu 16 Oct 2008"
-.SH NAME
-genrestr_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3genrestr_d\fP
-.BI "-f" " conf.gro "
-.BI "-n" " index.ndx "
-.BI "-o" " posre.itp "
-.BI "-of" " freeze.ndx "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-fc" " vector "
-.BI "-freeze" " real "
-.BI "-[no]disre" ""
-.BI "-disre_dist" " real "
-.BI "-disre_frac" " real "
-.BI "-disre_up2" " real "
-.BI "-[no]constr" ""
-.SH DESCRIPTION
-genrestr 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: position restraints only work for the one molecule at a time.
-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.
-
-
-The -of option produces an index file that can be used for
-freezing atoms. In this case the input file must be a pdb file.
-
-
-With the
-.B -disre
-option half a matrix of distance restraints
-is generated instead of position restraints. With this matrix, that
-one typically would apply to C-alpha atoms in a protein, one can
-maintain the overall conformation of a protein without tieing it to
-a specific position (as with position restraints).
-.SH FILES
-.BI "-f" " conf.gro"
-.B Input
- Generic structure: gro g96 pdb tpr tpb tpa xml
-
-.BI "-n" " index.ndx"
-.B Input, Opt.
- Index file
-
-.BI "-o" " posre.itp"
-.B Output
- Include file for topology
-
-.BI "-of" " freeze.ndx"
-.B Output, Opt.
- Index file
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 0"
- Set the nicelevel
-
-.BI "-fc" " vector" " 1000 1000 1000"
- force constants (kJ mol-1 nm-2)
-
-.BI "-freeze" " real" " 0 "
- if the -of option or this one is given an index file will be written containing atom numbers of all atoms that have a B-factor less than the level given here
-
-.BI "-[no]disre" "no "
- Generate a distance restraint matrix for all the atoms in index
-
-.BI "-disre_dist" " real" " 0.1 "
- Distance range around the actual distance for generating distance restraints
-
-.BI "-disre_frac" " real" " 0 "
- Fraction of distance to be used as interval rather than a fixed distance. If the fraction of the distance that you specify here is less than the distance given in the previous option, that one is used instead.
-
-.BI "-disre_up2" " real" " 1 "
- Distance between upper bound for distance restraints, and the distance at which the force becomes constant (see manual)
-
-.BI "-[no]constr" "no "
- Generate a constraint matrix rather than distance restraints
-
+++ /dev/null
-.TH gmxcheck_d 1 "Thu 16 Oct 2008"
-.SH NAME
-gmxcheck_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3gmxcheck_d\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 "-n" " index.ndx "
-.BI "-m" " doc.tex "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-vdwfac" " real "
-.BI "-bonlo" " real "
-.BI "-bonhi" " real "
-.BI "-tol" " real "
-.BI "-[no]ab" ""
-.BI "-lastener" " string "
-.SH DESCRIPTION
-gmxcheck reads a trajectory (
-.B .trj
-,
-.B .trr
-or
-
-.B .xtc
-), an energy file (
-.B .ene
-or
-.B .edr
-)
-or an index file (
-.B .ndx
-)
-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.
-
-
-If an index file is given it's contents will be sumamrized.
-
-
-If both a trajectory and a tpr file are given (with
-.B -s1
-)
-the program will check whether the bond lengths defined in the tpr
-file are indeed correct in the trajectory. If not you may have
-non-matching files due to e.g. deshuffling or due to problems with
-virtual sites. With these flags, gmxcheck provides a quick check for such problems.
-
-The program can compare run two input (
-.B .tpr
-,
-.B .tpb
-or
-
-.B .tpa
-) files
-when both
-.B -s1
-and
-.B -s2
-are supplied.
-Similarly a pair of trajectory files can be compared (using the
-.B -f2
-
-option), or a pair of energy files (using the
-.B -e2
-option).
-
-
-For free energy simulations the A and B state topology from one
-run input file can be compared with options
-.B -s1
-and
-.B -ab
-.
-
-
-In case the
-.B -m
-flag is given a LaTeX file will be written
-consisting a rough outline for a methods section for a paper.
-.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 xml
-
-.BI "-s2" " top2.tpr"
-.B Input, Opt.
- Generic run input: tpr tpb tpa xml
-
-.BI "-c" " topol.tpr"
-.B Input, Opt.
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
-
-.BI "-e" " ener.edr"
-.B Input, Opt.
- Generic energy: edr ene
-
-.BI "-e2" " ener2.edr"
-.B Input, Opt.
- Generic energy: edr ene
-
-.BI "-n" " index.ndx"
-.B Input, Opt.
- Index file
-
-.BI "-m" " doc.tex"
-.B Output, Opt.
- LaTeX file
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 0"
- 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" " 0.001 "
- Relative tolerance for comparing real values defined as 2*(a-b)/(|a|+|b|)
-
-.BI "-[no]ab" "no "
- Compare the A and B topology from one file
-
-.BI "-lastener" " string" " "
- Last energy term to compare (if not given all are tested). It makes sense to go up until the Pressure.
-
+++ /dev/null
-.TH gmxdump_d 1 "Thu 16 Oct 2008"
-.SH NAME
-gmxdump_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3gmxdump_d\fP
-.BI "-s" " topol.tpr "
-.BI "-f" " traj.xtc "
-.BI "-e" " ener.edr "
-.BI "-om" " grompp.mdp "
-.BI "-[no]h" ""
-.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.
-
-
-When requesting to dump a topology file the program will dump
-the processed topology, since not all original information is maintained
-in tpr files.
-.SH FILES
-.BI "-s" " topol.tpr"
-.B Input, Opt.
- Generic run input: tpr tpb tpa xml
-
-.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
-
-.BI "-om" " grompp.mdp"
-.B Output, Opt.
- grompp input file with MD parameters
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.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_d 1 "Thu 16 Oct 2008"
-.SH NAME
-grompp_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3grompp_d\fP
-.BI "-f" " grompp.mdp "
-.BI "-po" " mdout.mdp "
-.BI "-c" " conf.gro "
-.BI "-r" " conf.gro "
-.BI "-rb" " conf.gro "
-.BI "-n" " index.ndx "
-.BI "-p" " topol.top "
-.BI "-pp" " processed.top "
-.BI "-o" " topol.tpr "
-.BI "-t" " traj.trr "
-.BI "-e" " ener.edr "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-[no]v" ""
-.BI "-time" " real "
-.BI "-[no]rmvsbds" ""
-.BI "-maxwarn" " int "
-.BI "-[no]zero" ""
-.BI "-[no]renum" ""
-.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 uses the atom names from the topology file. The atom names
-in the coordinate file (option
-.B -c
-) are only read to generate
-warnings when they do not match the atom names in the topology.
-Note that the atom names are irrelevant for the simulation as
-only the atom types are used for generating interaction parameters.
-
-
-grompp calls a preprocessor to resolve includes, macros
-etcetera. By default we use the cpp in your path. To specify a different macro-preprocessor (e.g. m4) or alternative location
-you can put a line in your parameter file specifying the path
-to that program. 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 restraining will be done
-with respect to the conformation from the
-.B -c
-option.
-For free energy calculation the the coordinates for the B topology
-can be supplied with
-.B -rb
-, otherwise they will be equal to
-those of the A topology.
-
-
-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. An energy file can be supplied with
-
-.B -e
-to have exact restarts when using pressure and/or
-Nose-Hoover temperature coupling. For an exact restart do not forget
-to turn off velocity generation and turn on unconstrained starting
-when constraints are present in the system.
-If you want to continue a crashed run, it is
-easier to use
-.B tpbconv
-.
-
-
-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
-virtual site 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 -rmvsbds
-. Additionally,
-all constraints for distances which will be constant anyway because
-of virtual site constructions will be removed. If any constraints remain
-which involve virtual sites, 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, Opt.
- 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 xml
-
-.BI "-r" " conf.gro"
-.B Input, Opt.
- Generic structure: gro g96 pdb tpr tpb tpa xml
-
-.BI "-rb" " conf.gro"
-.B Input, Opt.
- Generic structure: gro g96 pdb tpr tpb tpa xml
-
-.BI "-n" " index.ndx"
-.B Input, 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 xml
-
-.BI "-t" " traj.trr"
-.B Input, Opt.
- Full precision trajectory: trr trj
-
-.BI "-e" " ener.edr"
-.B Input, Opt.
- Generic energy: edr ene
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.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 "-[no]rmvsbds" "yes "
- Remove constant bonded interactions with virtual sites
-
-.BI "-maxwarn" " int" " 0"
- Number of allowed warnings during input processing
-
-.BI "-[no]zero" "no "
- Set parameters for bonded interactions without defaults to zero instead of generating an error
-
-.BI "-[no]renum" "yes "
- Renumber atomtypes and minimize number of atomtypes
-
+++ /dev/null
-.TH highway_d 1 "Thu 16 Oct 2008"
-.SH NAME
-highway_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3highway_d\fP
-.BI "-f" " highway.dat "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.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. A sample
-input file is in $GMXDATA/top/highway.dat
-.SH FILES
-.BI "-f" " highway.dat"
-.B Input
- Generic data file
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 0"
- Set the nicelevel
-
+++ /dev/null
-.TH make_edi_d 1 "Thu 16 Oct 2008"
-.SH NAME
-make_edi_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3make_edi_d\fP
-.BI "-f" " eigenvec.trr "
-.BI "-eig" " eigenval.xvg "
-.BI "-s" " topol.tpr "
-.BI "-n" " index.ndx "
-.BI "-tar" " target.gro "
-.BI "-ori" " origin.gro "
-.BI "-o" " sam.edi "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-[no]xvgr" ""
-.BI "-mon" " string "
-.BI "-linfix" " string "
-.BI "-linacc" " string "
-.BI "-flood" " string "
-.BI "-radfix" " string "
-.BI "-radacc" " string "
-.BI "-radcon" " string "
-.BI "-outfrq" " int "
-.BI "-logfrq" " int "
-.BI "-slope" " real "
-.BI "-maxedsteps" " int "
-.BI "-deltaF0" " real "
-.BI "-deltaF" " real "
-.BI "-tau" " real "
-.BI "-eqsteps" " int "
-.BI "-Eflnull" " real "
-.BI "-T" " real "
-.BI "-alpha" " real "
-.BI "-linstep" " string "
-.BI "-accdir" " string "
-.BI "-radstep" " real "
-.BI "-[no]restrain" ""
-.BI "-[no]hesse" ""
-.BI "-[no]harmonic" ""
-.SH DESCRIPTION
-
-.B make_edi
-generates an ED-sampling input file to be used with mdrun
-based on eigenvectors of a covariance matrix (
-.B g_covar
-) or from a
-Normal Modes anaysis (
-.B g_nmeig
-).
-ED-sampling can be used to manipulate the position along collective coordinates
-(eigenvectors) of (biological) macromolecules during a simulation. Particularly,
-it may be used to enhance the sampling efficiency of MD simulations by stimulating
-the system to explore new regions along these collective coordinates. A number
-of different algorithms are implemented to drive the system along the eigenvectors
-(
-.B -linfix
-,
-.B -linacc
-,
-.B -radfix
-,
-.B -radacc
-,
-.B -radcon
-),
-to keep the position along a certain (set of) coordinate(s) fixed (
-.B -linfix
-),
-or to only monitor the projections of the positions, velocities and forces onto
-these coordinates(
-.B -mon
-).
-
-References:
-
-A. Amadei, A.B.M. Linssen, B.L. de Groot, D.M.F. van Aalten and
-H.J.C. Berendsen; An efficient method for sampling the essential subspace
-of proteins., J. Biomol. Struct. Dyn. 13:615-626 (1996)
-
-B.L. de Groot, A. Amadei, D.M.F. van Aalten and H.J.C. Berendsen;
-Towards an exhaustive sampling of the configurational spaces of the
-two forms of the peptide hormone guanylin,J. Biomol. Struct. Dyn. 13 : 741-751 (1996)
-
-B.L. de Groot, A.Amadei, R.M. Scheek, N.A.J. van Nuland and H.J.C. Berendsen;
-An extended sampling of the configurational space of HPr from E. coli
-PROTEINS: Struct. Funct. Gen. 26: 314-322 (1996)
-
-
-You will be prompted for one or more index groups that correspond to the eigenvectors,
-reference structure, target positions, etc.
-
-
-
-.B -mon
-: monitor projections of x, v and f onto selected eigenvectors.
-
-
-
-.B -linfix
-: perform fixed-step linear expansion along selected eigenvectors.
-
-
-
-.B -linacc
-: perform acceptance linear expansion along selected eigenvectors.
-(steps in the desired directions will be accepted, others will be rejected).
-
-
-
-.B -radfix
-: perform fixed-step radius expansion along selected eigenvectors.
-
-
-
-.B -radacc
-: perform acceptance radius expansion along selected eigenvectors.
-(steps in the desired direction will be accepted, others will be rejected).
-Note: by default the starting MD structure will be taken as origin of the first
-expansion cycle for radius expansion. If
-.B -ori
-is specified, you will be able
-to read in a structure file that defines an external origin.
-
-
-.B -radcon
-: perform acceptance radius contraction along selected eigenvectors
-towards a target structure specified with
-.B -tar
-.NOTE: each eigenvector can be selected only once.
-
-
-.B -outfrq
-: frequency (in steps) of writing out projections etc.
-
-
-
-.B -logfrq
-: frequency (in steps) of writing out statistics to log file.
-
-
-
-.B -slope
-: minimal slope in acceptance radius expansion. A new expansion
-cycle will be started if the spontaneous increase of the radius (in nm/step)
-is less than the value specified.
-
-
-.B -maxedsteps
-: maximum number of steps per cycle in radius expansion
-before a new cycle is started.
-
-Note on the parallel implementation: since ED sampling is a 'global' thing
-(collective coordinates etc), at least on the 'protein' side, ED sampling
-is not very parallel-friendly from an implentation point of view (it would
-require much extra communication to fully parallelize the algorithms).
-Fortunately, however, a typical parallel protein simulation in gromacs has
-most or all protein coordinates on one processor (the master) and has only
-other atoms (solvent, lipid, ions etc) on the other processors. With such a
-setup, ED sampling will still work. If the atoms over which ED sampling should
-be performed are spread over multiple processors, a fatal error will result.
-
-All output of mdrun (specify with -eo) is written to a .edo file (some extra
-information is written to the log file of mdrun too, actually). The .edo format
-is a simple ASCII file that should be easy to parse with standard unix tools
-like awk. A script (parse_edo) can be downloaded from contribution section at
- www.gromacs.org to extract information from the
-.edo files for your convinience. In short, the header defines which information
-can be expected in the rest of the .edo file. After the header, per step the
-following information is present:
-
-
-* the step number
-
-* RMSD (for atoms in fitting prior to calculating ED constr.)
-
-* projections of the positions onto selected eigenvectors
-
-* projections of the velocities onto selected eigenvectors
-
-* projections of the forces onto selected eigenvectors
-
-
-
-All projections are in the same order as in the header, so if you have e.g.
-2 groups (say one group over which acceptance radius expansion is performed,
-and another for which the projections are merely monitored) then you first
-get the position projections for each of the 2 groups, then the velocities
-and then the forces. Radii are not explicitly written to the .edo file, as
-they can be readily projected back from the positions. Alternatively, radii
-may be 'grepped from the log file.
-
-
-
-
-
-FLOODING:
-
-
-with -flood you can specify which eigenvectors are used to compute a flooding potential,
-which will lead to extra forces expelling the structure out of the region described
-by the covariance matrix. if you switch -restrain the potential is inverted and the structure
-is kept in that region
-
-
-
-the origin is normally the average structure stored in the eigvec.trr file
-it can be changed with -ori to an arbitrary position in configurational space
-with -tau , -deltaF0 and -Eflnull you control the flooding strength
-Efl is the flooding strength, it is updated according to the rule of adaptive flooding
-tau is the time constant of adaptive flooding, high tau means slow adaption (i.e. growth)
-deltaF0 is the flooding strength you want to reach after tau ps of simulation
-to use constant Efl set -tau to zero
-
-
-
--alpha is a fudge parameter to control the width of the flooding potential. A value of 2 has been found
-to give good results for most standard cases in flooding of proteins
-alpha basically accounts for incomplete sampling, if you sampled further the width of the ensemble would
-increase, this is mimicked by alpha1for restraining alpha1 can give you smaller width in the restraining potentialRESTART and FLOODING:
-If you want to restart a crashed flooding simulation please find the values deltaF and Efl in
-the output file and write them with your texteditor into the .edi file under DELTA_F0 and EFL_NULL
-.SH FILES
-.BI "-f" " eigenvec.trr"
-.B Input
- Full precision trajectory: trr trj
-
-.BI "-eig" " eigenval.xvg"
-.B Input, Opt.
- xvgr/xmgr file
-
-.BI "-s" " topol.tpr"
-.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
-
-.BI "-n" " index.ndx"
-.B Input, Opt.
- Index file
-
-.BI "-tar" " target.gro"
-.B Input, Opt.
- Generic structure: gro g96 pdb tpr tpb tpa xml
-
-.BI "-ori" " origin.gro"
-.B Input, Opt.
- Generic structure: gro g96 pdb tpr tpb tpa xml
-
-.BI "-o" " sam.edi"
-.B Output
- ED sampling input
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 0"
- Set the nicelevel
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.BI "-mon" " string" " "
- Indices of eigenvectors for projections of x, v and f (e.g. 1,2-5,9) or 1-100:10 means 1 11 21 31 ... 91
-
-.BI "-linfix" " string" " "
- Indices of eigenvectors for fixed increment linear sampling
-
-.BI "-linacc" " string" " "
- Indices of eigenvectors for acceptance linear sampling
-
-.BI "-flood" " string" " "
- Indices of eigenvectors for flooding
-
-.BI "-radfix" " string" " "
- Indices of eigenvectors for fixed increment radius expansion
-
-.BI "-radacc" " string" " "
- Indices of eigenvectors for acceptance radius expansion
-
-.BI "-radcon" " string" " "
- Indices of eigenvectors for acceptance radius contraction
-
-.BI "-outfrq" " int" " 100"
- freqency (in steps) of writing output in .edo file
-
-.BI "-logfrq" " int" " 100"
- frequency (in steps) of writing to log
-
-.BI "-slope" " real" " 0 "
- minimal slope in acceptance radius expamsion
-
-.BI "-maxedsteps" " int" " 0"
- max nr of steps per cycle
-
-.BI "-deltaF0" " real" " 150 "
- target destabilization energy - used for flooding
-
-.BI "-deltaF" " real" " 0 "
- start deltaF with this parameter - default 0, i.g. nonzero values only needed for restart
-
-.BI "-tau" " real" " 0.1 "
- coupling constant for adaption of flooding strength according to deltaF0, 0 = infinity i.e. constant flooding strength
-
-.BI "-eqsteps" " int" " 0"
- number of steps to run without any perturbations
-
-.BI "-Eflnull" " real" " 0 "
- this is the starting value of the flooding strength. The flooding strength is updated according to the adaptive flooding scheme. To use a constant flooding strength use -tau 0.
-
-.BI "-T" " real" " 300 "
- T is temperature, the value is needed if you want to do flooding
-
-.BI "-alpha" " real" " 1 "
- scale width of gaussian flooding potential with alpha2
-
-.BI "-linstep" " string" " "
- Stepsizes (nm/step) for fixed increment linear sampling (put in quotes! "1.0 2.3 5.1 -3.1")
-
-.BI "-accdir" " string" " "
- Directions for acceptance linear sampling - only sign counts! (put in quotes! "-1 +1 -1.1")
-
-.BI "-radstep" " real" " 0 "
- Stepsize (nm/step) for fixed increment radius expansion
-
-.BI "-[no]restrain" "no "
- use the flooding potential with inverted sign - effects as quasiharmonic restraining potential
-
-.BI "-[no]hesse" "no "
- the eigenvectors and eigenvalues are from a Hesse matrix
-
-.BI "-[no]harmonic" "no "
- the eigenvalues are interpreted as spring constant
-
+++ /dev/null
-.TH make_ndx_d 1 "Thu 16 Oct 2008"
-.SH NAME
-make_ndx_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3make_ndx_d\fP
-.BI "-f" " conf.gro "
-.BI "-n" " index.ndx "
-.BI "-o" " index.ndx "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-natoms" " 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.
-When a run input file is supplied you can also select on atom type.
-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, Opt.
- Generic structure: gro g96 pdb tpr tpb tpa xml
-
-.BI "-n" " index.ndx"
-.B Input, Opt., Mult.
- Index file
-
-.BI "-o" " index.ndx"
-.B Output
- Index file
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 0"
- Set the nicelevel
-
-.BI "-natoms" " int" " 0"
- set number of atoms (default: read from coordinate or index file)
-
+++ /dev/null
-.TH mdrun_d 1 "Thu 16 Oct 2008"
-.SH NAME
-mdrun_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3mdrun_d\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 "-field" " field.xvg "
-.BI "-table" " table.xvg "
-.BI "-tablep" " tablep.xvg "
-.BI "-tableb" " table.xvg "
-.BI "-rerun" " rerun.xtc "
-.BI "-tpi" " tpi.xvg "
-.BI "-tpid" " tpidist.xvg "
-.BI "-ei" " sam.edi "
-.BI "-eo" " sam.edo "
-.BI "-j" " wham.gct "
-.BI "-jo" " bam.gct "
-.BI "-ffout" " gct.xvg "
-.BI "-devout" " deviatie.xvg "
-.BI "-runav" " runaver.xvg "
-.BI "-px" " pullx.xvg "
-.BI "-pf" " pullf.xvg "
-.BI "-mtx" " nm.mtx "
-.BI "-dn" " dipole.ndx "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-deffnm" " string "
-.BI "-[no]xvgr" ""
-.BI "-[no]pd" ""
-.BI "-dd" " vector "
-.BI "-nt" " int "
-.BI "-npme" " int "
-.BI "-ddorder" " enum "
-.BI "-rdd" " real "
-.BI "-rcon" " real "
-.BI "-[no]dlb" ""
-.BI "-[no]sum" ""
-.BI "-[no]v" ""
-.BI "-[no]compact" ""
-.BI "-[no]seppot" ""
-.BI "-[no]reprod" ""
-.BI "-multi" " int "
-.BI "-replex" " int "
-.BI "-reseed" " int "
-.BI "-[no]glas" ""
-.BI "-[no]ionize" ""
-.SH DESCRIPTION
-The mdrun program is the main computational chemistry engine
-within GROMACS. Obviously, it performs Molecular Dynamics simulations,
-but it can also perform Stochastic Dynamics, Energy Minimization,
-test particle insertion or (re)calculation of energies.
-Normal mode analysis is another option. In this case mdrun
-builds a Hessian matrix from single conformation.
-For usual Normal Modes-like calculations, make sure that
-the structure provided is properly energy-minimized.
-The generated matrix can be diagonalized by g_nmeig.
-
-
-The mdrun program reads the run input file (
-.B -s
-)
-and distributes the topology over nodes if needed.
-mdrun produces at least four output files.
-A single log file (
-.B -g
-) is written, unless the option
-
-.B -seppot
-is used, in which case each node writes a log file.
-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.
-Optionally coordinates can be written to a compressed trajectory file
-(
-.B -x
-).
-
-
-The option
-.B -dgdl
-is only used when free energy perturbation is
-turned on.
-
-
-When mdrun is started using MPI with more than 1 node, parallelization
-is used. By default domain decomposition is used, unless the
-.B -pd
-
-option is set, which selects particle decomposition.
-
-
-With domain decomposition, the spatial decomposition can be set
-with option
-.B -dd
-. By default mdrun selects a good decomposition.
-The user only needs to change this when there are errors due to missing
-interactions, or when the system is very inhomogeneous.
-When PME is used, separate nodes can be assigned to do only the PME
-calculation; this is computationally more efficient starting at
-about 12 nodes. The number of PME nodes is set with option
-
-.B -npme
-, this can not be more than half of the nodes.
-By default mdrun makes a guess for the number of PME
-nodes when the number of nodes is 12 or larger or when the PME grid
-x or y dimension is not divisible by the number of nodes, but the user
-should optimize npme. Performance statistics on this issue are written
-at the end of the log file.
-Dynamic load balancing can be turned on with the option
-.B -dlb
-,
-which can give a significant performance improvement,
-especially for inhomogeneous systems. The only disadvantage of
-dynamic load balancing is that runs are no longer binary reproducible,
-but in most cases this is not important.
-All distances required for two-body bonded interactions should be within
-the non-bonded cut-off distance;
-all distances required for multi-body bonded interactions should be
-within the smallest cell size. If this is not the case mdrun terminates
-with an error message. By default mdrun sets the minimum cell size to
-half the cut-off distance or the maximum distance required
-for constraints, whichever is larger.
-Option
-.B -rdd
-can be used to set the allowed distance for
-multi-body bonded interactions or also for two-body bonded interactions
-when
-.B -rdd
-is larger than the non-bonded cut-off.
-With dynamic load balancing option
-.B -rdd
-also sets
-the lower limit for the domain decomposition cell sizes.
-When constraints are present, option [TT-rcon
-influences
-the cell size limit as well.
-Atoms connected by NC constraints, where NC is the LINCS order plus 1,
-should not be beyond the smallest cell size. A error message is
-generated when this happens and the user should change the decomposition
-or decrease the LINCS order and increase the number of LINCS iterations.
-By default mdrun estimates the minimum cell size required for P-LINCS
-in a conservative fashion. For high parallelization it can be useful
-to set the distance required for P-LINCS with the option
-.B -rcon
-.
-Finally the option
-.B -nosum
-can be used to only sum the energies
-at every neighbor search step. This can improve performance for highly
-parallel simulations, where this global communication step becomes
-the bottleneck. This option is currently not allowed when
-an extended ensemble thermostat or barostat is used.
-
-
-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.
-
-
-When user-defined potential functions have been selected in the
-
-.B .mdp
-file the
-.B -table
-option is used to pass mdrun
-a formatted table with potential functions. The file is read from
-either the current directory or from the GMXLIB directory.
-A number of pre-formatted tables are presented in the GMXLIB dir,
-for 6-8, 6-9, 6-10, 6-11, 6-12 Lennard Jones potentials with
-normal Coulomb.
-When pair interactions are present a separate table for pair interaction
-functions is read using the
-.B -tablep
-option.
-
-
-When tabulated bonded functions are present in the topology,
-interaction functions are read using the
-.B -tableb
-option.
-For each different tabulated interaction type the table file name is
-modified in a different way: before the file extension an underscore is
-appended, then a b for bonds, an a for angles or a d for dihedrals
-and finally the table number of the interaction type.
-
-
-The options
-.B -pi
-,
-.B -po
-,
-.B -pd
-,
-.B -pn
-are used
-for potential of mean force calculations and umbrella sampling.
-See manual.
-
-
-With
-.B -multi
-multiple systems are simulated in parallel.
-As many input files are required as the number of systems.
-The system number is appended to the run input and each output filename,
-for instance topol.tpr becomes topol0.tpr, topol1.tpr etc.
-The number of nodes per system is the total number of nodes
-divided by the number of systems.
-One use of this option is for NMR refinement: when distance
-or orientation restraints are present these can be ensemble averaged
-over all the systems.
-
-
-With
-.B -replex
-replica exchange is attempted every given number
-of steps. The number of replicas is set with the
-.B -multi
-option,
-see above.
-All run input files should use a different coupling temperature,
-the order of the files is not important. The random seed is set with
-
-.B -reseed
-. The velocities are scaled and neighbor searching
-is performed after every exchange.
-
-
-Finally some experimental algorithms can be tested when the
-appropriate options have been given. Currently under
-investigation are: polarizability, glass simulations
-and X-Ray bombardments.
-
-
-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 xml
-
-.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 xml
-
-.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 "-field" " field.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.BI "-table" " table.xvg"
-.B Input, Opt.
- xvgr/xmgr file
-
-.BI "-tablep" " tablep.xvg"
-.B Input, Opt.
- xvgr/xmgr file
-
-.BI "-tableb" " table.xvg"
-.B Input, Opt.
- xvgr/xmgr file
-
-.BI "-rerun" " rerun.xtc"
-.B Input, Opt.
- Generic trajectory: xtc trr trj gro g96 pdb
-
-.BI "-tpi" " tpi.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.BI "-tpid" " tpidist.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.BI "-ei" " sam.edi"
-.B Input, Opt.
- ED sampling input
-
-.BI "-eo" " sam.edo"
-.B Output, Opt.
- ED sampling output
-
-.BI "-j" " wham.gct"
-.B Input, Opt.
- General coupling stuff
-
-.BI "-jo" " bam.gct"
-.B Output, Opt.
- General coupling stuff
-
-.BI "-ffout" " gct.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.BI "-devout" " deviatie.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.BI "-runav" " runaver.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.BI "-px" " pullx.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.BI "-pf" " pullf.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.BI "-mtx" " nm.mtx"
-.B Output, Opt.
- Hessian matrix
-
-.BI "-dn" " dipole.ndx"
-.B Output, Opt.
- Index file
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-deffnm" " string" " "
- Set the default filename for all file options
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.BI "-[no]pd" "no "
- Use particle decompostion
-
-.BI "-dd" " vector" " 0 0 0"
- Domain decomposition grid, 0 is optimize
-
-.BI "-nt" " int" " 1"
- Number of threads to start on each node
-
-.BI "-npme" " int" " -1"
- Number of separate nodes to be used for PME, -1 is guess
-
-.BI "-ddorder" " enum" " interleave"
- DD node order:
-.B interleave
-,
-.B pp_pme
-or
-.B cartesian
-
-
-.BI "-rdd" " real" " 0 "
- The minimum distance for DD communication (nm)
-
-.BI "-rcon" " real" " 0 "
- Maximum distance for P-LINCS (nm), 0 is estimate
-
-.BI "-[no]dlb" "no "
- Use dynamic load balancing (only with DD)
-
-.BI "-[no]sum" "yes "
- Sum the energies at every step
-
-.BI "-[no]v" "no "
- Be loud and noisy
-
-.BI "-[no]compact" "yes "
- Write a compact log file
-
-.BI "-[no]seppot" "no "
- Write separate V and dVdl terms for each interaction type and node to the log file(s)
-
-.BI "-[no]reprod" "no "
- Try to avoid optimizations that affect binary reproducibility
-
-.BI "-multi" " int" " 0"
- Do multiple simulations in parallel
-
-.BI "-replex" " int" " 0"
- Attempt replica exchange every steps
-
-.BI "-reseed" " int" " -1"
- Seed for replica exchange, -1 is generate a seed
-
-.BI "-[no]glas" "no "
- Do glass simulation with special long range corrections
-
-.BI "-[no]ionize" "no "
- Do a simulation including the effect of an X-Ray bombardment on your system
-
+++ /dev/null
-.TH mk_angndx_d 1 "Thu 16 Oct 2008"
-.SH NAME
-mk_angndx_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3mk_angndx_d\fP
-.BI "-s" " topol.tpr "
-.BI "-n" " angle.ndx "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-type" " enum "
-.BI "-[no]hyd" ""
-.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 xml
-
-.BI "-n" " angle.ndx"
-.B Output
- Index file
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 0"
- Set the nicelevel
-
-.BI "-type" " enum" " angle"
- Type of angle:
-.B angle
-,
-.B g96-angle
-,
-.B dihedral
-,
-.B improper
-,
-.B ryckaert-bellemans
-or
-.B phi-psi
-
-
-.BI "-[no]hyd" "yes "
- Include angles with atoms with mass 1.5
-
+++ /dev/null
-.TH ngmx_d 1 "Thu 16 Oct 2008"
-.SH NAME
-ngmx_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3ngmx_d\fP
-.BI "-f" " traj.xtc "
-.BI "-s" " topol.tpr "
-.BI "-n" " index.ndx "
-.BI "-[no]h" ""
-.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 xml
-
-.BI "-n" " index.ndx"
-.B Input, Opt.
- Index file
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 0"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- Only use frame when t MOD dt = first time (ps)
-
-.SH KNOWN PROBLEMS
-\- Balls option does not work
-
-\- Some times dumps core without a good reason
-
+++ /dev/null
-.TH pdb2gmx_d 1 "Thu 16 Oct 2008"
-.SH NAME
-pdb2gmx_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3pdb2gmx_d\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 "-nice" " int "
-.BI "-[no]merge" ""
-.BI "-ff" " string "
-.BI "-water" " enum "
-.BI "-[no]inter" ""
-.BI "-[no]ss" ""
-.BI "-[no]ter" ""
-.BI "-[no]lys" ""
-.BI "-[no]arg" ""
-.BI "-[no]asp" ""
-.BI "-[no]glu" ""
-.BI "-[no]gln" ""
-.BI "-[no]his" ""
-.BI "-angle" " real "
-.BI "-dist" " real "
-.BI "-[no]una" ""
-.BI "-[no]ignh" ""
-.BI "-[no]missing" ""
-.BI "-[no]v" ""
-.BI "-posrefc" " real "
-.BI "-vsite" " enum "
-.BI "-[no]heavyh" ""
-.BI "-[no]deuterate" ""
-.SH DESCRIPTION
-This program reads a pdb file, 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.
-
-
-
-The force fields in the distribution are currently:
-
-
-oplsaa OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
-
-G43b1 GROMOS96 43b1 Vacuum Forcefield
-
-G43a1 GROMOS96 43a1 Forcefield
-
-G43a2 GROMOS96 43a2 Forcefield (improved alkane dihedrals)
-
-G45a3 GROMOS96 45a3 Forcefield
-
-G53a5 GROMOS96 53a5 Forcefield
-
-G53a6 GROMOS96 53a6 Forcefield
-
-gmx Gromacs Forcefield (a modified GROMOS87, see manual)
-
-encads Encad all-atom force field, using scaled-down vacuum charges
-
-encadv Encad all-atom force field, using full solvent charges
-
-
-The corresponding data files can be found in the library directory
-with names like ffXXXX.YYY. Check chapter 5 of the manual for more
-information about file formats. By default the forcefield selection
-is interactive, but you can use the
-.B -ff
-option to specify
-one of the short names above on the command line instead. In that
-case pdb2gmx just looks for the corresponding 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 definition, this can be useful for connecting chains
-with a disulfide brigde or intermolecular distance restraints.
-
-
-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.
-
-
-
-The option
-.B -vsite
-removes hydrogen and fast improper dihedral
-motions. Angular and out-of-plane motions can be removed by changing
-hydrogens into virtual sites 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 virtual sites, elminating the fast improper dihedral
-fluctuations in these rings. Note that in this case all other hydrogen
-atoms are also converted to virtual sites. The mass of all atoms that are
-converted into virtual sites, 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.
-.SH FILES
-.BI "-f" " eiwit.pdb"
-.B Input
- Generic structure: gro g96 pdb tpr tpb tpa xml
-
-.BI "-o" " conf.gro"
-.B Output
- Generic structure: gro g96 pdb xml
-
-.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 xml
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 0"
- Set the nicelevel
-
-.BI "-[no]merge" "no "
- Merge chains into one molecule definition
-
-.BI "-ff" " string" " select"
- Force field, interactive by default. Use -h for information.
-
-.BI "-water" " enum" " spc"
- Water model to use: with GROMOS we recommend SPC, with OPLS, TIP4P:
-.B spc
-,
-.B spce
-,
-.B tip3p
-,
-.B tip4p
-,
-.B tip5p
-or
-.B f3c
-
-
-.BI "-[no]inter" "no "
- Set the next 8 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]arg" "no "
- Interactive Arganine 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]gln" "no "
- Interactive Glutamine selection, iso neutral
-
-.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]ignh" "no "
- Ignore hydrogen atoms that are in the pdb file
-
-.BI "-[no]missing" "no "
- Continue when atoms are missing, dangerous
-
-.BI "-[no]v" "no "
- Be slightly more verbose in messages
-
-.BI "-posrefc" " real" " 1000 "
- Force constant for position restraints
-
-.BI "-vsite" " enum" " none"
- Convert atoms to virtual sites:
-.B none
-,
-.B hydrogens
-or
-.B 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_d 1 "Thu 16 Oct 2008"
-.SH NAME
-protonate_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3protonate_d\fP
-.BI "-s" " topol.tpr "
-.BI "-f" " traj.xtc "
-.BI "-n" " index.ndx "
-.BI "-o" " protonated.xtc "
-.BI "-[no]h" ""
-.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 xml
-
-.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 "-nice" " int" " 0"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- Only use frame when t MOD dt = first time (ps)
-
+++ /dev/null
-.TH sigeps_d 1 "Thu 16 Oct 2008"
-.SH NAME
-sigeps_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3sigeps_d\fP
-.BI "-o" " potje.xvg "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-[no]w" ""
-.BI "-[no]xvgr" ""
-.BI "-c6" " real "
-.BI "-cn" " real "
-.BI "-pow" " int "
-.BI "-sig" " real "
-.BI "-eps" " real "
-.BI "-A" " real "
-.BI "-B" " real "
-.BI "-C" " real "
-.BI "-qi" " real "
-.BI "-qj" " real "
-.BI "-sigfac" " real "
-.SH DESCRIPTION
-Sigeps is a simple utility that converts c6/c12 or c6/cn combinations
-to sigma and epsilon, or vice versa. It can also plot the potential
-in file. In addition it makes an approximation of a Buckingham potential
-to a Lennard Jones potential.
-.SH FILES
-.BI "-o" " potje.xvg"
-.B Output
- xvgr/xmgr file
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 0"
- Set the nicelevel
-
-.BI "-[no]w" "no "
- View output xvg, xpm, eps and pdb files
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.BI "-c6" " real" " 0.001 "
- c6
-
-.BI "-cn" " real" " 1e-06 "
- constant for repulsion
-
-.BI "-pow" " int" " 12"
- power of the repulsion term
-
-.BI "-sig" " real" " 0.3 "
- sig
-
-.BI "-eps" " real" " 1 "
- eps
-
-.BI "-A" " real" " 100000"
- Buckingham A
-
-.BI "-B" " real" " 32 "
- Buckingham B
-
-.BI "-C" " real" " 0.001 "
- Buckingham C
-
-.BI "-qi" " real" " 0 "
- qi
-
-.BI "-qj" " real" " 0 "
- qj
-
-.BI "-sigfac" " real" " 0.7 "
- Factor in front of sigma for starting the plot
-
+++ /dev/null
-.TH tpbconv_d 1 "Thu 16 Oct 2008"
-.SH NAME
-tpbconv_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3tpbconv_d\fP
-.BI "-s" " topol.tpr "
-.BI "-f" " traj.trr "
-.BI "-e" " ener.edr "
-.BI "-n" " index.ndx "
-.BI "-o" " tpxout.tpr "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-time" " real "
-.BI "-extend" " real "
-.BI "-until" " real "
-.BI "-[no]zeroq" ""
-.BI "-[no]cont" ""
-.SH DESCRIPTION
-tpbconv can edit run input files in three 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.
-When pressure and/or Nose-Hoover temperature coupling is used
-an energy file can be supplied to get an exact continuation
-of the original run.
-
-
-
-.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
-.
-
-.B 3rd.
-by setting the charges of a specified group
-to zero. This is useful when doing free energy estimates
-using the LIE (Linear Interactio Energy) method.
-.SH FILES
-.BI "-s" " topol.tpr"
-.B Input
- Generic run input: tpr tpb tpa xml
-
-.BI "-f" " traj.trr"
-.B Input, Opt.
- Full precision trajectory: trr trj
-
-.BI "-e" " ener.edr"
-.B Input, Opt.
- Generic energy: edr ene
-
-.BI "-n" " index.ndx"
-.B Input, Opt.
- Index file
-
-.BI "-o" " tpxout.tpr"
-.B Output
- Generic run input: tpr tpb tpa xml
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.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]zeroq" "no "
- Set the charges of a group (from the index) to zero
-
-.BI "-[no]cont" "yes "
- For exact continuation, the constraints should not be solved before the first step
-
+++ /dev/null
-.TH trjcat_d 1 "Thu 16 Oct 2008"
-.SH NAME
-trjcat_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3trjcat_d\fP
-.BI "-f" " traj.xtc "
-.BI "-o" " trajout.xtc "
-.BI "-n" " index.ndx "
-.BI "-demux" " remd.xvg "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-tu" " enum "
-.BI "-[no]xvgr" ""
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-dt" " time "
-.BI "-prec" " int "
-.BI "-[no]vel" ""
-.BI "-[no]settime" ""
-.BI "-[no]sort" ""
-.BI "-[no]keeplast" ""
-.BI "-[no]cat" ""
-.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. Using
-.B -cat
-you can simply paste several files
-together without removal of frames with identical time stamps.
-
-
-One important option is inferred when the output file is amongst the
-input files. In that case that particular file will be appended to
-which implies you do not need to store double the amount of data.
-Obviously the file to append to has to be the one with lowest starting
-time since one can only append at the end of a file.
-
-
-If the
-.B -demux
-option is given, the N trajectories that are
-read, are written in another order as specified in the xvg file.The xvg file should contain something like:
-
-
-0 0 1 2 3 4 5
-
-2 1 0 2 3 5 4
-
-Where the first number is the time, and subsequent numbers point to
-trajectory indices.
-The frames corresponding to the numbers present at the first line
-are collected into the output trajectory. If the number of frames in
-the trajectory does not match that in the xvg file then the program
-tries to be smart. Beware.
-.SH FILES
-.BI "-f" " traj.xtc"
-.B Input, Mult.
- Generic trajectory: xtc trr trj gro g96 pdb
-
-.BI "-o" " trajout.xtc"
-.B Output, Mult.
- Generic trajectory: xtc trr trj gro g96 pdb
-
-.BI "-n" " index.ndx"
-.B Input, Opt.
- Index file
-
-.BI "-demux" " remd.xvg"
-.B Input, Opt.
- xvgr/xmgr file
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-tu" " enum" " ps"
- Time unit:
-.B ps
-,
-.B fs
-,
-.B ns
-,
-.B us
-,
-.B ms
-or
-.B s
-
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.BI "-b" " time" " -1 "
- First time to use (ps)
-
-.BI "-e" " time" " -1 "
- Last time to use (ps)
-
-.BI "-dt" " time" " 0 "
- Only write frame when t MOD dt = first time (ps)
-
-.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)
-
-.BI "-[no]keeplast" "no "
- keep overlapping frames at end of trajectory
-
-.BI "-[no]cat" "no "
- do not discard double time frames
-
+++ /dev/null
-.TH trjconv_d 1 "Thu 16 Oct 2008"
-.SH NAME
-trjconv_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3trjconv_d\fP
-.BI "-f" " traj.xtc "
-.BI "-o" " trajout.xtc "
-.BI "-s" " topol.tpr "
-.BI "-n" " index.ndx "
-.BI "-fr" " frames.ndx "
-.BI "-sub" " cluster.ndx "
-.BI "-drop" " drop.xvg "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-tu" " enum "
-.BI "-[no]w" ""
-.BI "-[no]xvgr" ""
-.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 "-boxcenter" " enum "
-.BI "-box" " vector "
-.BI "-trans" " vector "
-.BI "-shift" " vector "
-.BI "-fit" " enum "
-.BI "-ndec" " int "
-.BI "-[no]vel" ""
-.BI "-[no]force" ""
-.BI "-trunc" " time "
-.BI "-exec" " string "
-.BI "-[no]app" ""
-.BI "-split" " time "
-.BI "-[no]sep" ""
-.BI "-nzero" " int "
-.BI "-[no]ter" ""
-.BI "-dropunder" " real "
-.BI "-dropover" " real "
-.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.
-change the periodicity representation
-
-
-.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
-)
-
-
-.B 9.
-cut the trajectory in small subtrajectories according
-to information in an index file. This allows subsequent analysis of
-the subtrajectories that could, for example be the result of a
-cluster analysis. Use option
-.B -sub
-.
-This assumes that the entries in the index file are frame numbers and
-dumps each group in the index file to a separate trajectory file.
-
-
-.B 10.
-select frames within a certain range of a quantity given
-in an
-.B .xvg
-file.
-
-
-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.
-
-
-Option
-.B -sep
-can be used to write every frame to a seperate
-.gro, .g96 or .pdb file, default all frames all written to one 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 mol
-puts the center of mass of molecules in the box.
-
-*
-.B res
-puts the center of mass of residues in the box.
-
-*
-.B atom
-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 cluster
-clusters all the atoms in the selected index
-such that they are all closest to the center of mass of the cluster
-which is iteratively updated. Note that this will only give meaningful
-results if you in fact have a cluster. Luckily that can be checked
-afterwards using a trajectory viewer. Note also that if your molecules
-are broken this will not work either.
-
-*
-.B whole
-only makes broken molecules whole.
-
-
-Option
-.B -ur
-sets the unit cell representation for options
-
-.B mol
-,
-.B res
-and
-.B atom
-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. The center for options
-.B tric
-and
-.B compact
-
-is
-.B tric
-(see below), unless the option
-.B -boxcenter
-
-is set differently.
-
-
-Option
-.B -center
-centers the system in the box. The user can
-select the group which is used to determine the geometrical center.
-Option
-.B -boxcenter
-sets the location of the center of the box
-for options
-.B -pbc
-and
-.B -center
-. The center options are:
-
-.B tric
-: half of the sum of the box vectors,
-
-.B rect
-: half of the box diagonal,
-
-.B zero
-: zero.
-Use option
-.B -pbc mol
-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). For making smooth movies the program
-.B g_filter
-
-can reduce the number of frames while using low-pass frequency
-filtering, this reduces aliasing of high frequency motions.
-
-
-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.
-
-
-Option
-.B -drop
-reads an
-.B .xvg
-file with times and values.
-When options
-.B -dropunder
-and/or
-.B -dropover
-are set,
-frames with a value below and above the value of the respective options
-will not be written.
-.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 xml
-
-.BI "-n" " index.ndx"
-.B Input, Opt.
- Index file
-
-.BI "-fr" " frames.ndx"
-.B Input, Opt.
- Index file
-
-.BI "-sub" " cluster.ndx"
-.B Input, Opt.
- Index file
-
-.BI "-drop" " drop.xvg"
-.B Input, Opt.
- xvgr/xmgr file
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-tu" " enum" " ps"
- Time unit:
-.B ps
-,
-.B fs
-,
-.B ns
-,
-.B us
-,
-.B ms
-or
-.B s
-
-
-.BI "-[no]w" "no "
- View output xvg, xpm, eps and pdb files
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.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 (see help text for full description):
-.B none
-,
-.B mol
-,
-.B res
-,
-.B atom
-,
-.B nojump
-,
-.B cluster
-or
-.B whole
-
-
-.BI "-ur" " enum" " rect"
- Unit-cell representation:
-.B rect
-,
-.B tric
-or
-.B compact
-
-
-.BI "-[no]center" "no "
- Center atoms in box
-
-.BI "-boxcenter" " enum" " tric"
- Center for -pbc and -center:
-.B tric
-,
-.B rect
-or
-.B zero
-
-
-.BI "-box" " vector" " 0 0 0"
- Size for new cubic box (default: read from input)
-
-.BI "-trans" " vector" " 0 0 0"
- All coordinates will be translated by trans. This can advantageously be combined with -pbc mol -ur compact.
-
-.BI "-shift" " vector" " 0 0 0"
- All coordinates will be shifted by framenr*shift
-
-.BI "-fit" " enum" " none"
- Fit molecule to ref structure in the structure file:
-.B none
-,
-.B rot+trans
-,
-.B rotxy+transxy
-,
-.B translation
-or
-.B progressive
-
-
-.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 "-split" " time" " 0 "
- Start writing new file when t MOD split = first time (ps)
-
-.BI "-[no]sep" "no "
- Write each frame to a separate .gro, .g96 or .pdb file
-
-.BI "-nzero" " int" " 0"
- Prepend file number in case you use the -sep flag with this number of zeroes
-
-.BI "-[no]ter" "no "
- Use 'TER' in pdb file as end of frame in stead of default 'ENDMDL'
-
-.BI "-dropunder" " real" " 0 "
- Drop all frames below this value
-
-.BI "-dropover" " real" " 0 "
- Drop all frames above this value
-
+++ /dev/null
-.TH trjorder_d 1 "Thu 16 Oct 2008"
-.SH NAME
-trjorder_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3trjorder_d\fP
-.BI "-f" " traj.xtc "
-.BI "-s" " topol.tpr "
-.BI "-n" " index.ndx "
-.BI "-o" " ordered.xtc "
-.BI "-nshell" " nshell.xvg "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-dt" " time "
-.BI "-[no]xvgr" ""
-.BI "-na" " int "
-.BI "-da" " int "
-.BI "-[no]com" ""
-.BI "-r" " real "
-.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.
-
-
-
-If the output file is a pdb file, the distance to the reference target
-will be stored in the B-factor field in order to color with e.g. rasmol.
-
-
-
-With option
-.B -nshell
-the number of molecules within a shell
-of radius
-.B -r
-around the refernce group are printed.
-.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 xml
-
-.BI "-n" " index.ndx"
-.B Input, Opt.
- Index file
-
-.BI "-o" " ordered.xtc"
-.B Output, Opt.
- Generic trajectory: xtc trr trj gro g96 pdb
-
-.BI "-nshell" " nshell.xvg"
-.B Output, Opt.
- xvgr/xmgr file
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 19"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- Only use frame when t MOD dt = first time (ps)
-
-.BI "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.BI "-na" " int" " 3"
- Number of atoms in a molecule
-
-.BI "-da" " int" " 1"
- Atom used for the distance calculation
-
-.BI "-[no]com" "no "
- Use the distance to the center of mass of the reference group
-
-.BI "-r" " real" " 0 "
- Cutoff used for the distance calculation when computing the number of molecules in a shell around e.g. a protein
-
+++ /dev/null
-.TH wheel_d 1 "Thu 16 Oct 2008"
-.SH NAME
-wheel_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3wheel_d\fP
-.BI "-f" " nnnice.dat "
-.BI "-o" " plot.eps "
-.BI "-[no]h" ""
-.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 "-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_d 1 "Thu 16 Oct 2008"
-.SH NAME
-x2top_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3x2top_d\fP
-.BI "-f" " conf.gro "
-.BI "-o" " out.top "
-.BI "-r" " out.rtp "
-.BI "-d" " qpol.dat "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-ff" " string "
-.BI "-[no]v" ""
-.BI "-nexcl" " int "
-.BI "-[no]H14" ""
-.BI "-[no]alldih" ""
-.BI "-[no]remdih" ""
-.BI "-[no]pairs" ""
-.BI "-[no]pol" ""
-.BI "-name" " string "
-.BI "-[no]pbc" ""
-.BI "-[no]pdbq" ""
-.BI "-btol" " real "
-.BI "-[no]param" ""
-.BI "-[no]round" ""
-.BI "-kb" " real "
-.BI "-kt" " real "
-.BI "-kp" " real "
-.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.
-
-
-When
-.B -param
-is set, equilibrium distances and angles
-and force constants will be printed in the topology for all
-interactions. The equilibrium distances and angles are taken
-from the input coordinates, the force constant are set with
-command line options.The force fields supported currently are:
-
-
-oplsaa OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
-
-
-The corresponding data files can be found in the library directory
-with names like ffXXXX.YYY. Check chapter 5 of the manual for more
-information about file formats. By default the forcefield selection
-is interactive, but you can use the
-.B -ff
-option to specify
-one of the short names above on the command line instead. In that
-case pdb2gmx just looks for the corresponding file.
-
-
-An optional file containing atomname charge polarizability can be
-given with the
-.B -d
-flag.
-.SH FILES
-.BI "-f" " conf.gro"
-.B Input
- Generic structure: gro g96 pdb tpr tpb tpa xml
-
-.BI "-o" " out.top"
-.B Output, Opt.
- Topology file
-
-.BI "-r" " out.rtp"
-.B Output, Opt.
- Residue Type file used by pdb2gmx
-
-.BI "-d" " qpol.dat"
-.B Input, Opt.
- Generic data file
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 0"
- Set the nicelevel
-
-.BI "-ff" " string" " select"
- Select the force field for your simulation.
-
-.BI "-[no]v" "no "
- Generate verbose output in the top file.
-
-.BI "-nexcl" " int" " 3"
- Number of exclusions
-
-.BI "-[no]H14" "yes "
- Use 3rd neighbour interactions for hydrogen atoms
-
-.BI "-[no]alldih" "no "
- Generate all proper dihedrals
-
-.BI "-[no]remdih" "no "
- Remove dihedrals on the same bond as an improper
-
-.BI "-[no]pairs" "yes "
- Output 1-4 interactions (pairs) in topology file
-
-.BI "-[no]pol" "no "
- Output polarization terms for those atoms where alpha 0
-
-.BI "-name" " string" " ICE"
- Name of your molecule
-
-.BI "-[no]pbc" "yes "
- Use periodic boundary conditions.
-
-.BI "-[no]pdbq" "no "
- Use the B-factor supplied in a pdb file for the atomic charges
-
-.BI "-btol" " real" " 0.1 "
- Relative tolerance for determining whether two atoms are bonded.
-
-.BI "-[no]param" "yes "
- Print parameters in the output
-
-.BI "-[no]round" "yes "
- Round off measured values
-
-.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)
-
-.SH KNOWN PROBLEMS
-\- The atom type selection is primitive. Virtually no chemical knowledge is used
-
-\- 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_d 1 "Thu 16 Oct 2008"
-.SH NAME
-xpm2ps_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3xpm2ps_d\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 "-nice" " int "
-.BI "-[no]w" ""
-.BI "-[no]frame" ""
-.BI "-title" " enum "
-.BI "-[no]yonce" ""
-.BI "-legend" " enum "
-.BI "-diag" " enum "
-.BI "-size" " real "
-.BI "-bx" " real "
-.BI "-by" " real "
-.BI "-rainbow" " enum "
-.BI "-gradient" " vector "
-.BI "-skip" " int "
-.BI "-[no]zeroline" ""
-.BI "-legoffset" " int "
-.BI "-combine" " enum "
-.BI "-cmin" " real "
-.BI "-cmax" " real "
-.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.
-
-
-When no
-.B m2p
-file is supplied, many setting are set by
-command line options. The most important option is
-.B -size
-
-which sets the size of the whole matrix in postscript units.
-This option can be overridden with the
-.B -bx
-and
-.B -by
-
-options (and the corresponding parameters in the
-.B m2p
-file),
-which set the size of a single matrix element.
-
-
-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
-.
-In this case, a new color map will be generated with
-a red gradient for negative numbers and a blue for positive.
-If the color coding and legend labels of both matrices are identical,
-only one legend will be displayed, else two separate legends are
-displayed.
-With
-.B -combine
-an alternative operation can be selected
-to combine the matrices. The output range is automatically set
-to the actual range of the combined matrix. This can be overridden
-with
-.B -cmin
-and
-.B -cmax
-.
-
-
-
-.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 "-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:
-.B top
-,
-.B once
-,
-.B ylabel
-or
-.B none
-
-
-.BI "-[no]yonce" "no "
- Show y-label only once
-
-.BI "-legend" " enum" " both"
- Show legend:
-.B both
-,
-.B first
-,
-.B second
-or
-.B none
-
-
-.BI "-diag" " enum" " first"
- Diagonal:
-.B first
-,
-.B second
-or
-.B none
-
-
-.BI "-size" " real" " 400 "
- Horizontal size of the matrix in ps units
-
-.BI "-bx" " real" " 0 "
- Element x-size, overrides -size (also y-size when -by is not set)
-
-.BI "-by" " real" " 0 "
- Element y-size
-
-.BI "-rainbow" " enum" " no"
- Rainbow colors, convert white to:
-.B no
-,
-.B blue
-or
-.B red
-
-
-.BI "-gradient" " vector" " 0 0 0"
- Re-scale colormap to a smooth gradient from white {1,1,1} to {r,g,b}
-
-.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
-
-.BI "-legoffset" " int" " 0"
- Skip first N colors from xpm file for the legend
-
-.BI "-combine" " enum" " halves"
- Combine two matrices:
-.B halves
-,
-.B add
-,
-.B sub
-,
-.B mult
-or
-.B div
-
-
-.BI "-cmin" " real" " 0 "
- Minimum for combination output
-
-.BI "-cmax" " real" " 0 "
- Maximum for combination output
-
+++ /dev/null
-.TH xrama_d 1 "Thu 16 Oct 2008"
-.SH NAME
-xrama_d
-.B VERSION 3.3.99_development_20071104
-.SH SYNOPSIS
-\f3xrama_d\fP
-.BI "-f" " traj.xtc "
-.BI "-s" " topol.tpr "
-.BI "-[no]h" ""
-.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 xml
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 0"
- Set the nicelevel
-
-.BI "-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " 0 "
- Only use frame when t MOD dt = first time (ps)
-
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff