--- /dev/null
+.TH anadock 1 "Sun 25 Jan 2004"
+.SH NAME
+anadock
+.B VERSION 3.2.0
+.SH SYNOPSIS
+\f3anadock\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]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]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 cdist 1 "Sun 25 Jan 2004"
+.SH NAME
+cdist
+.B VERSION 3.2.0
+.SH SYNOPSIS
+\f3cdist\fP
+.BI "-s" " topol.tpr "
+.BI "-g" " cdist.log "
+.BI "-q" " eiwit.pdb "
+.BI "-d" " nnnice.dat "
+.BI "-o" " cdist.dat "
+.BI "-n" " hbond.ndx "
+.BI "-dom" " domain.ndx "
+.BI "-[no]h" ""
+.BI "-nice" " int "
+.BI "-[no]engh" ""
+.BI "-bm" " real "
+.BI "-am" " real "
+.BI "-pm" " real "
+.BI "-rr" " real "
+.BI "-ar" " real "
+.BI "-er" " real "
+.BI "-vm" " real "
+.BI "-lm" " real "
+.BI "-il" " real "
+.BI "-dm" " real "
+.BI "-im" " real "
+.BI "-nm" " real "
+.BI "-hm" " real "
+.BI "-hb" " real "
+.BI "-[no]bon" ""
+.BI "-[no]nb" ""
+.BI "-measure" " real "
+.BI "-maxdist" " real "
+.BI "-[no]add" ""
+.BI "-[no]vir" ""
+.BI "-sm" " enum "
+.SH DESCRIPTION
+cdist read a
+.B tpx
+file and dumps an input file for disco.
+Bond lengths etc. are read from the topology. Pairs of atoms that can
+form hydrogen bonds are given a lowest possible distance of
+
+.B hblen
+(can be specified by the user). Other nonbonded pairs
+take their minimum distance from the Lennard Jones parameters
+(at the combined sigma).
+
+
+The program uses proper dihedrals to give a distance too, as minimum
+respectively maximum the
+.I cis
+and
+.I trans
+configurations
+are taken. It is therefore beneficial to use the
+.B -alldih
+option
+of
+.B pdb2gmx
+to generate a topology with all dihedrals in there.
+If the optional pdb file is given, weights are read from the occupancy
+field, so that
+not all atoms are part of the disco run, only those of which one of the
+weights is non-zero.
+
+
+If the option -engh is on (default) bond lengths and angles etc. are
+read from another database, which is basically the Engh-Huber data
+but refined to be completely self consistent. The database name is
+refi_aa.dat and it resides in the $GMXLIB directory, or in the current
+directory.
+
+
+The program can read a file with distances from NMR distance restraints
+(-d option). Note that these distance are treated slightly different
+in the disco program, and therefore these distance should be NMR
+derived distance restraints only.
+
+
+Furthermore, the program can read an index file with hydrogen bond
+information as generated by
+.B g_hbond
+. This is then used to set
+tighter restraints on the hydrogen bonded atoms than on the other
+non bonded atom pairs, in order to maintain secondary structure.
+This option is useful only in combination with the
+.B -measure
+
+option, when a sensible structure is known.
+
+
+The option
+.B -dom
+can be used to release distances bounds between
+different domains to the lower bounds given by Van der Waals contacts.
+This way, different domains can move independently, but without
+overlapping. The index file should contain domains that do not overlap
+with each other.
+.SH FILES
+.BI "-s" " topol.tpr"
+.B Input
+ Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+
+.BI "-g" " cdist.log"
+.B Output
+ Log file
+
+.BI "-q" " eiwit.pdb"
+.B Input, Opt.
+ Protein data bank file
+
+.BI "-d" " nnnice.dat"
+.B Input, Opt.
+ Generic data file
+
+.BI "-o" " cdist.dat"
+.B Output
+ Generic data file
+
+.BI "-n" " hbond.ndx"
+.B Input, Opt.
+ Index file
+
+.BI "-dom" " domain.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]engh" " yes"
+ Use the Engh&Huber parameters for bond-lengths etc.
+
+.BI "-bm" " real" " 0.01"
+ Relative margin for bond lengths
+
+.BI "-am" " real" " 0.01"
+ Relative margin for bond angle lengths
+
+.BI "-pm" " real" " 0.01"
+ Relative margin for peptidebond dihedrals
+
+.BI "-rr" " real" " 0.01"
+ Relative margin to keep rings flat (trp,tyr,phe,hisb)
+
+.BI "-ar" " real" " 0.01"
+ Relative margin for arginine
+
+.BI "-er" " real" " 0.01"
+ Relative margin for asn and gln
+
+.BI "-vm" " real" " 0.01"
+ Relative margin for valine (0 disables)
+
+.BI "-lm" " real" " 0.01"
+ Relative margin for leucine (0 disables)
+
+.BI "-il" " real" " 0.03"
+ Relative margin for isoleucine (0 disables)
+
+.BI "-dm" " real" " 0.01"
+ !inactive! Relative margin for dihedral lengths
+
+.BI "-im" " real" " 0.01"
+ Relative margin for improper dihedral lengths
+
+.BI "-nm" " real" " 0.05"
+ Relative margin for nonbonded lower bounds
+
+.BI "-hm" " real" " 0.02"
+ Relative margin for hydrogen bonded atoms, which must be specified in an index file, as generated by g_hbond
+
+.BI "-hb" " real" " 2.3"
+ Shortest possible distance for a hydrogen bond (in Angstrom!)
+
+.BI "-[no]bon" " yes"
+ Make bonded distance constraints
+
+.BI "-[no]nb" " yes"
+ Make nonbonded distance constraints (lower bound only)
+
+.BI "-measure" " real" " 0"
+ Add (nonbonded) distances by examining all atoms within the distance given (in Angstrom), and using the margin given by the -nm option.
+
+.BI "-maxdist" " real" " 0"
+ Maximum distance between any pair of atoms
+
+.BI "-[no]add" " no"
+ Write restraints in format of additional restraints for disco
+
+.BI "-[no]vir" " no"
+ Use virtual particles
+
+.BI "-sm" " enum" " none"
+ Smoothing: none, tri (Using triangle inequality), or tetra (Partial tetrangle inequaliy):
+.B none
+,
+.B tri
+or
+.B tetra
+
+
--- /dev/null
+.TH disco 1 "Sun 25 Jan 2004"
+.SH NAME
+disco
+.B VERSION 3.2.0
+.SH SYNOPSIS
+\f3disco\fP
+.BI "-g" " disco.log "
+.BI "-f" " conf.gro "
+.BI "-d" " cdist.dat "
+.BI "-do" " distout.dat "
+.BI "-c" " out.gro "
+.BI "-center" " out.gro "
+.BI "-n" " index.ndx "
+.BI "-o" " structs.xtc "
+.BI "-keep" " unconverged.xtc "
+.BI "-viol" " vvv.pdb "
+.BI "-[no]h" ""
+.BI "-nice" " int "
+.BI "-nf" " int "
+.BI "-nit" " int "
+.BI "-[no]v" ""
+.BI "-[no]chiral" ""
+.BI "-[no]pep" ""
+.BI "-[no]lower" ""
+.BI "-[no]weighted" ""
+.BI "-[no]dump" ""
+.BI "-[no]cubic" ""
+.BI "-[no]explicit" ""
+.BI "-[no]fit" ""
+.BI "-nbcheck" " int "
+.BI "-nstprint" " int "
+.BI "-ranlist" " int "
+.BI "-[no]ranlistfirst" ""
+.BI "-lowdev" " real "
+.BI "-seed" " int "
+.BI "-box" " vector "
+.BI "-grow" " int "
+.SH DESCRIPTION
+disco reads a topology (tpr) file and runs distance geometry
+calculations based on the distances defined in the
+distance-restraints section of the topology. An appropriate tpr
+file may be generated by the cdist program.
+
+
+The algorithm is the CONCOORD algorithm of De Groot et al.,
+which in turn is derived from the SHAKE alogrithm.
+
+
+A parallel version of disco is under development whihc uses a
+master-slave approach. Slaves work asynchronously, and it is no
+problem when nodes are not equally fast, or when a node dies,
+unless it is the master node.
+.SH FILES
+.BI "-g" " disco.log"
+.B Output
+ Log file
+
+.BI "-f" " conf.gro"
+.B Input
+ Generic structure: gro g96 pdb tpr tpb tpa xml
+
+.BI "-d" " cdist.dat"
+.B Input
+ Generic data file
+
+.BI "-do" " distout.dat"
+.B Output, Opt.
+ Generic data file
+
+.BI "-c" " out.gro"
+.B Input
+ Generic structure: gro g96 pdb xml
+
+.BI "-center" " out.gro"
+.B Input, Opt.
+ Generic structure: gro g96 pdb xml
+
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
+.BI "-o" " structs.xtc"
+.B Output
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-keep" " unconverged.xtc"
+.B Output, Opt.
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-viol" " vvv.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 "-nf" " int" " 10"
+ Number of structures to generate
+
+.BI "-nit" " int" " 1000"
+ Max number of iterations for a structure to converge
+
+.BI "-[no]v" " yes"
+ Be verbosive
+
+.BI "-[no]chiral" " yes"
+ Check chirality during disco-ing
+
+.BI "-[no]pep" " yes"
+ Flip all cis-peptide bonds automatically to trans
+
+.BI "-[no]lower" " no"
+ Use lower bounds only for nonbondeds.
+
+.BI "-[no]weighted" " no"
+ Use weighted disco. The STX file must be a pdb file in this case and weights are read from the occupancy field
+
+.BI "-[no]dump" " no"
+ Dump the trajectory of the shaking to testX.xtc file where X is the structure number.
+
+.BI "-[no]cubic" " no"
+ Generate coordinates in a cubic box, rather than rectangular
+
+.BI "-[no]explicit" " no"
+ Use explicit updating of positions if the sum of deviations is smaller than lowdev
+
+.BI "-[no]fit" " no"
+ Fit output structures to reference structure in tpx file
+
+.BI "-nbcheck" " int" " 1"
+ Check non-bonded interactions every N steps
+
+.BI "-nstprint" " int" " 1"
+ Print number of violations every N steps
+
+.BI "-ranlist" " int" " 0"
+ Update list order to avoid bias every n steps
+
+.BI "-[no]ranlistfirst" " yes"
+ Randomize list once before shaking
+
+.BI "-lowdev" " real" " 0.05"
+ Low deviation [Sum of distance deviation per atom in nm] beyond which nonbondeds are done every step
+
+.BI "-seed" " int" " 1997"
+ Seed for the random number generator
+
+.BI "-box" " vector" " 2 2 2"
+ Boxsize (nm) for generating random coordinates
+
+.BI "-grow" " int" " 0"
+ Number of steps after which Van der Waals lower bounds grow from 0 to the real lower bounds. If this is 0 (default), the Van der Waals lower bounds are in effect from the beginning
+
--- /dev/null
+.TH ffscan 1 "Sun 25 Jan 2004"
+.SH NAME
+ffscan
+.B VERSION 3.2.0
+.SH SYNOPSIS
+\f3ffscan\fP
+.BI "-s" " topol.tpr "
+.BI "-g" " md.log "
+.BI "-table" " table.xvg "
+.BI "-parm" " params.dat "
+.BI "-ga" " genalg.dat "
+.BI "-c" " junk.gro "
+.BI "-e" " junk.edr "
+.BI "-o" " junk.trr "
+.BI "-[no]h" ""
+.BI "-nice" " int "
+.BI "-tol" " real "
+.BI "-fmax" " real "
+.BI "-[no]comb" ""
+.BI "-npow" " real "
+.BI "-[no]logeps" ""
+.BI "-[no]v" ""
+.BI "-epot" " real "
+.BI "-fepot" " real "
+.BI "-pres" " real "
+.BI "-fpres" " real "
+.BI "-fmsf" " real "
+.BI "-molsize" " int "
+.BI "-nmol" " int "
+.SH DESCRIPTION
+The ffscan program performs a single point energy and force calculation
+in which the force field is modified. This way a range of parameters can
+be changed and tested for reproduction of e.g. quantum chemical or
+experimental data. A grid scan over the parameters is done as specified
+using command line arguments. All parameters that reproduce the energy
+within a given absolute tolerance are printed to a log file.
+
+
+Obviously polarizable models can be used, and shell optimisation is
+performed if necessary. Also, like in mdrun table functions can be used
+for user defined potential functions.
+
+
+If the option -ga with appropriate file is passed, a genetic algorithm will
+be used rather than a grid scan.
+.SH FILES
+.BI "-s" " topol.tpr"
+.B Input
+ Generic run input: tpr tpb tpa xml
+
+.BI "-g" " md.log"
+.B Output
+ Log file
+
+.BI "-table" " table.xvg"
+.B Input, Opt.
+ xvgr/xmgr file
+
+.BI "-parm" " params.dat"
+.B Input
+ Generic data file
+
+.BI "-ga" " genalg.dat"
+.B Input, Opt.
+ Generic data file
+
+.BI "-c" " junk.gro"
+.B Output
+ Coordinate file in Gromos-87 format
+
+.BI "-e" " junk.edr"
+.B Output
+ Generic energy: edr ene
+
+.BI "-o" " junk.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 "-tol" " real" " 0.1"
+ Energy tolerance (kJ/mol) (zero means everything is printed)
+
+.BI "-fmax" " real" " 100"
+ Force tolerance (zero means everything is printed)
+
+.BI "-[no]comb" " yes"
+ Use combination rules
+
+.BI "-npow" " real" " 12"
+ Power for LJ in case of table use
+
+.BI "-[no]logeps" " no"
+ Use a logarithmic scale for epsilon
+
+.BI "-[no]v" " no"
+ Be loud and noisy
+
+.BI "-epot" " real" " 0"
+ Target energy (kJ/mol)
+
+.BI "-fepot" " real" " 1"
+ Factor for scaling energy violations (0 turns energy contribution off)
+
+.BI "-pres" " real" " 1"
+ Value for reference pressure
+
+.BI "-fpres" " real" " 0.1"
+ Factor for scaling pressure violations (0 turns pressure contribution off)
+
+.BI "-fmsf" " real" " 0.1"
+ Factor for scaling mean square force violations (0 turns MSF contribution off)
+
+.BI "-molsize" " int" " 1"
+ Number of atoms per molecule
+
+.BI "-nmol" " int" " 1"
+ Number of molecules (Epot is divided by this value!)
+
--- /dev/null
+.TH g_clustsize 1 "Sun 25 Jan 2004"
+.SH NAME
+g_clustsize
+.B VERSION 3.2.0
+.SH SYNOPSIS
+\f3g_clustsize\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 "-[no]h" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-tu" " enum "
+.BI "-[no]w" ""
+.BI "-cut" " real "
+.BI "-[no]mol" ""
+.BI "-nskip" " int "
+.BI "-nlevels" " 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.
+.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
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " -1"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " -1"
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " -1"
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-tu" " enum" " ps"
+ Time unit:
+.B ps
+,
+.B fs
+,
+.B ns
+,
+.B us
+,
+.B ms
+,
+.B s
+,
+.B m
+or
+.B h
+
+
+.BI "-[no]w" " no"
+ View output xvg, xpm, eps and pdb files
+
+.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 "-nskip" " int" " 0"
+ Number of frames to skip between writing
+
+.BI "-nlevels" " int" " 20"
+ Number of levels of grey in xpm output
+
+.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_filter 1 "Sun 25 Jan 2004"
+.SH NAME
+g_filter
+.B VERSION 3.2.0
+.SH SYNOPSIS
+\f3g_filter\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" " -1"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " -1"
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " -1"
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-[no]w" " no"
+ View output xvg, xpm, eps and pdb files
+
+.BI "-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_wham 1 "Sun 25 Jan 2004"
+.SH NAME
+g_wham
+.B VERSION 3.2.0
+.SH SYNOPSIS
+\f3g_wham\fP
+.BI "-o" " profile.xvg "
+.BI "-hist" " histo.xvg "
+.BI "-[no]h" ""
+.BI "-nice" " int "
+.BI "-[no]w" ""
+.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 "-min" " real" " 0"
+ 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" " 298"
+ Temperature
+
+.BI "-[no]flip" " no"
+ Combine halves of profile
+
+.BI "-tol" " real" " 0.01"
+ Tolerance
+
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff