+++ /dev/null
-.TH cdist 1 "Mon 29 Aug 2005"
-.SH NAME
-cdist
-.B VERSION 3.3_beta_20050823
-.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 "Mon 29 Aug 2005"
-.SH NAME
-disco
-.B VERSION 3.3_beta_20050823
-.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 ehole 1 "Thu 16 Oct 2008"
-.SH NAME
-ehole
-.B VERSION 4.0_rc1
-.SH SYNOPSIS
-\f3ehole\fP
-.BI "-g" " ehole.log "
-.BI "-sigel" " sigel.dat "
-.BI "-sigin" " siginel.dat "
-.BI "-eloss" " eloss.dat "
-.BI "-qtrans" " qtrans.dat "
-.BI "-band" " band-ener.dat "
-.BI "-thetael" " theta-el.dat "
-.BI "-o" " ehole.pdb "
-.BI "-histo" " histo.xvg "
-.BI "-radius" " radius.xvg "
-.BI "-gyrate" " gyrate.xvg "
-.BI "-mfp" " mfp.xvg "
-.BI "-nion" " nion.xvg "
-.BI "-ener" " ener.xvg "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-[no]xvgr" ""
-.BI "-maxparticle" " int "
-.BI "-maxstep" " int "
-.BI "-nsim" " int "
-.BI "-nsave" " int "
-.BI "-nana" " int "
-.BI "-seed" " int "
-.BI "-dt" " real "
-.BI "-rho" " real "
-.BI "-matom" " real "
-.BI "-fermi" " real "
-.BI "-gap" " real "
-.BI "-auger" " real "
-.BI "-dx" " real "
-.BI "-[no]test" ""
-.BI "-[no]force" ""
-.BI "-[no]hole" ""
-.BI "-[no]scatter" ""
-.BI "-nevent" " int "
-.BI "-evdist" " real "
-.BI "-size" " real "
-.SH DESCRIPTION
-ehole performs a molecular dynamics simulation of electrons and holes
-.SH FILES
-.BI "-g" " ehole.log"
-.B Output
- Log file
-
-.BI "-sigel" " sigel.dat"
-.B Input
- Generic data file
-
-.BI "-sigin" " siginel.dat"
-.B Input
- Generic data file
-
-.BI "-eloss" " eloss.dat"
-.B Input
- Generic data file
-
-.BI "-qtrans" " qtrans.dat"
-.B Input
- Generic data file
-
-.BI "-band" " band-ener.dat"
-.B Input
- Generic data file
-
-.BI "-thetael" " theta-el.dat"
-.B Input
- Generic data file
-
-.BI "-o" " ehole.pdb"
-.B Output
- Protein data bank file
-
-.BI "-histo" " histo.xvg"
-.B Output
- xvgr/xmgr file
-
-.BI "-radius" " radius.xvg"
-.B Output
- xvgr/xmgr file
-
-.BI "-gyrate" " gyrate.xvg"
-.B Output
- xvgr/xmgr file
-
-.BI "-mfp" " mfp.xvg"
-.B Output
- xvgr/xmgr file
-
-.BI "-nion" " nion.xvg"
-.B Output
- xvgr/xmgr file
-
-.BI "-ener" " ener.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 "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.BI "-maxparticle" " int" " 100"
- Maximum number of particles
-
-.BI "-maxstep" " int" " 100000"
- Number of integration steps
-
-.BI "-nsim" " int" " 1"
- Number of independent simulations writing to different output files
-
-.BI "-nsave" " int" " 1"
- Number of steps after which to save output. 0 means only when particles created. Final step is always written.
-
-.BI "-nana" " int" " 1"
- Number of steps after which to do analysis.
-
-.BI "-seed" " int" " 1993"
- Random seed
-
-.BI "-dt" " real" " 1e-05 "
- Integration time step (ps)
-
-.BI "-rho" " real" " 3.51 "
- Density of the sample (kg/l). Default is for Diamond
-
-.BI "-matom" " real" " 12.011"
- Mass (a.m.u.) of the atom in the solid. Default is C
-
-.BI "-fermi" " real" " 28.7 "
- Fermi energy (eV) of the sample. Default is for Diamond
-
-.BI "-gap" " real" " 5.46 "
- Band gap energy (eV) of the sample. Default is for Diamond
-
-.BI "-auger" " real" " 250 "
- Impact energy (eV) of first electron
-
-.BI "-dx" " real" " 0.05 "
- Distance between electron and hole when creating a pair
-
-.BI "-[no]test" "no "
- Test table aspects of the program rather than running it for real
-
-.BI "-[no]force" "no "
- Apply Coulomb/Repulsion forces
-
-.BI "-[no]hole" "no "
- Create electron-hole pairs rather than electrons only
-
-.BI "-[no]scatter" "yes "
- Do the scattering events
-
-.BI "-nevent" " int" " 1"
- Number of initial Auger electrons
-
-.BI "-evdist" " real" " 10000 "
- Average distance (A) between initial electronss
-
-.BI "-size" " real" " 0 "
- Size of the spherical system. If 0, then it is infinite
-
+++ /dev/null
-.TH ffscan 1 "Mon 29 Aug 2005"
-.SH NAME
-ffscan
-.B VERSION 3.3_beta_20050823
-.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 "-[no]xvgr" ""
-.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 "-[no]xvgr" " yes"
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.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 ffscan_d 1 "Thu 16 Oct 2008"
-.SH NAME
-ffscan_d
-.B VERSION 3.3.99_development_20070813
-.SH SYNOPSIS
-\f3ffscan_d\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 "-[no]xvgr" ""
-.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 "-[no]xvgr" "yes "
- Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-
-.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 genpr 1 "Thu 16 Oct 2008"
-.SH NAME
-genpr
-.B VERSION 3.3.99_development_20070215
-.SH SYNOPSIS
-\f3genpr\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 "
-.SH DESCRIPTION
-genpr produces an include file for a topology containing
-a list of atom numbers and three force constants for the
-X, Y and Z direction. A single isotropic force constant may
-be given on the command line instead of three components.
-
-
-WARNING: genpr only works for the first molecule.
-Position restraints are interactions within molecules, therefore
-they should be included within the correct
-.B [ moleculetype ]
-
-block in the topology. Since the atom numbers in every moleculetype
-in the topology start at 1 and the numbers in the input file for
-genpr number consecutively from 1, genpr will only produce a useful
-file for the first molecule.
-
-
-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.
-.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
-
+++ /dev/null
-.TH genvsites 1 "Thu 16 Oct 2008"
-.SH NAME
-genvsites
-.B VERSION 3.3.99_development_20070618
-.SH SYNOPSIS
-\f3genvsites\fP
-.BI "-c" " eiwit.gro "
-.BI "-o" " conf.gro "
-.BI "-p" " topol.top "
-.BI "-pp" " processed.top "
-.BI "-q" " topol.top "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-[no]v" ""
-.BI "-ff" " string "
-.BI "-vsite" " enum "
-.BI "-[no]heavyh" ""
-.BI "-[no]deuterate" ""
-.SH DESCRIPTION
-This program read a coordinate file and a topology file, adds
-virtual sites as indicated on the command line and writes out
-a new topology and coordinate file.
-.SH FILES
-.BI "-c" " eiwit.gro"
-.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 Input
- Topology file
-
-.BI "-pp" " processed.top"
-.B Output, Opt.
- Topology file
-
-.BI "-q" " topol.top"
-.B Output
- Topology file
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 0"
- Set the nicelevel
-
-.BI "-[no]v" "no "
- Be loud and noisy
-
-.BI "-ff" " string" " select"
- Force field, interactive by default. Use -h for information.
-
-.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 hrefify 1 "Thu 16 Oct 2008"
-.SH NAME
-hrefify
-.B VERSION 3.3.99_development_200800503
-.SH SYNOPSIS
-\f3hrefify\fP
-.BI "-l" " links.dat "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-f" " string "
-.BI "-o" " string "
-.BI "-e" " string "
-.BI "-t" " string "
-.SH DESCRIPTION
-hrefify adds href's for all the words in the input file which are not
-already hyperlinked and which appear in the file specified with the
-option
-.B -l
-.
-
-
-If the href's should call a script, text can be added
-with the
-.B -t
-option.
-.SH FILES
-.BI "-l" " links.dat"
-.B Input, Lib.
- Generic data file
-
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 0"
- Set the nicelevel
-
-.BI "-f" " string" " "
- HTML input
-
-.BI "-o" " string" " "
- HTML output
-
-.BI "-e" " string" " "
- Exclude a string from HREF's, when this option is not set, the filename without path and extension will be excluded from HREF's
-
-.BI "-t" " string" " "
- Insert a string in front of the href file name, useful for scripts
-
+++ /dev/null
-.TH options 1 "Thu 16 Oct 2008"
-.SH NAME
-options
-.B VERSION 3.3.99_development_200800503
-.SH SYNOPSIS
-\f3options\fP
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.SH DESCRIPTION
-All GROMACS programs have 6 standard options,
-of which some are hidden by default:
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 0"
- Set the nicelevel
-
-.SH KNOWN PROBLEMS
-\- If the configuration script found Motif or Lesstif on your system, you can use the graphical interface (if not, you will get an error):
-
-.B -X
-bool
-.B no
-Use dialog box GUI to edit command line options
-
-\- When compiled on an SGI-IRIX system, all GROMACS programs have an additional option:
-
-.B -npri
-int
-.B 0
-Set non blocking priority (try 128)
-
-\- Optional files are not used unless the option is set, in contrast to non optional files, where the default file name is used when the option is not set.
-
-\- All GROMACS programs will accept file options without a file extension or filename being specified. In such cases the default filenames will be used. With multiple input file types, such as generic structure format, the directory will be searched for files of each type with the supplied or default name. When no such file is found, or with output files the first file type will be used.
-
-\- All GROMACS programs with the exception of
-.B mdrun
-,
-.B nmrun
-and
-.B eneconv
-check if the command line options are valid. If this is not the case, the program will be halted.
-
-\- Enumerated options (enum) should be used with one of the arguments listed in the option description, the argument may be abbreviated. The first match to the shortest argument in the list will be selected.
-
-\- Vector options can be used with 1 or 3 parameters. When only one parameter is supplied the two others are also set to this value.
-
-\- For many GROMACS programs, the time options can be supplied in different time units, depending on the setting of the
-.B -tu
-option.
-
-\- All GROMACS programs can read compressed or g-zipped files. There might be a problem with reading compressed
-.B .xtc
-,
-.B .trr
-and
-.B .trj
-files, but these will not compress very well anyway.
-
-\- Most GROMACS programs can process a trajectory with less atoms than the run input or structure file, but only if the trajectory consists of the first n atoms of the run input or structure file.
-
-\- Many GROMACS programs will accept the
-.B -tu
-option to set the time units to use in output files (e.g. for
-.B xmgr
-graphs or
-.B xpm
-matrices) and in all time options.
-
+++ /dev/null
-.TH tune_dip 1 "Thu 16 Oct 2008"
-.SH NAME
-tune_dip
-.B VERSION 4.0_rc1
-.SH SYNOPSIS
-\f3tune_dip\fP
-.BI "-f" " moldip.dat "
-.BI "-d" " eemprops.dat "
-.BI "-o" " molprops.dat "
-.BI "-g" " charges.log "
-.BI "-x" " dipcorr.xvg "
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.BI "-[no]w" ""
-.BI "-[no]xvgr" ""
-.BI "-tol" " real "
-.BI "-maxiter" " int "
-.BI "-reinit" " int "
-.BI "-stol" " real "
-.BI "-qgen" " enum "
-.BI "-[no]fixenh" ""
-.BI "-j0" " real "
-.BI "-chi0" " real "
-.BI "-w0" " real "
-.BI "-j1" " real "
-.BI "-chi1" " real "
-.BI "-w1" " real "
-.BI "-fc" " real "
-.BI "-step" " real "
-.BI "-elem" " string "
-.BI "-seed" " int "
-.BI "-[no]random" ""
-.BI "-[no]zero" ""
-.BI "-[no]weight" ""
-.BI "-hfac" " real "
-.BI "-[no]opthfac" ""
-.BI "-slater_max" " int "
-.SH DESCRIPTION
-tune_dip read a series of molecules and corresponding experimental
-dipole moments from a file, and tunes parameters in an algorithm
-until the experimental dipole moments are reproduces by the
-charge generating algorithm SM in the gentop program.
-
-
-Minima and maxima for the parameters can be set, these are however
-not strictly enforced, but rather they are penalized with a harmonic
-function, for which the force constant can be set explicitly.
-
-
-At every reinit step parameters are changed by a random amount within
-the fraction set by step size, and within the boundaries given
-by the minima and maxima.
-
-
-The absolut dipole moment of a molecule remains unchanged if all the
-atoms swap the sign of the charge. To prevent this kind of mirror
-effects a penalty is added to the square deviation
-if hydrogen atoms have a negative charge. Similarly a penalty is
-added if atoms from row VI or VII in the periodic table have a positive
-charge. The penalty is equal to the force constant given on the command line
-time the square of the charge.
-
-
-One of the electronegativities (chi) is redundant in the optimization,
-only the relative values are meaningful.
-Therefore by default we fix the value for hydrogen to what is written
-in the eemprops.dat file (or whatever is given with the
--d
-.B flag).
-A suitable value would be 2.3, the original, value due to Pauling,
-this can by overridden by setting the
--nofixenh
-.B flag.
-.SH FILES
-.BI "-f" " moldip.dat"
-.B Input
- Generic data file
-
-.BI "-d" " eemprops.dat"
-.B Input, Opt.
- Generic data file
-
-.BI "-o" " molprops.dat"
-.B Output
- Generic data file
-
-.BI "-g" " charges.log"
-.B Output
- Log file
-
-.BI "-x" " dipcorr.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 "-tol" " real" " 0.001 "
- Tolerance for convergence in optimization
-
-.BI "-maxiter" " int" " 100"
- Max number of iterations for optimization
-
-.BI "-reinit" " int" " 0"
- After this many iterations the search vectors are randomized again. A vlue of 0 means this is never done at all.
-
-.BI "-stol" " real" " 1e-06 "
- If reinit is -1 then a reinit will be done as soon as the simplex size is below this treshold.
-
-.BI "-qgen" " enum" " SMp"
- Algorithm used for charge generation:
-.B SMp
-,
-.B SMpp
-,
-.B SMs
-,
-.B SMps
-,
-.B SMg
-or
-.B SMgs
-
-
-.BI "-[no]fixenh" "yes "
- Electronegativity for hydrogen. Set to FALSE if you want this variable as well, but read the help text above.
-
-.BI "-j0" " real" " 0 "
- Minimum value that J0 can obtain in fitting
-
-.BI "-chi0" " real" " 0 "
- Minimum value that Chi0 can obtain in fitting
-
-.BI "-w0" " real" " 0 "
- Minimum value that Radius can obtain in fitting
-
-.BI "-j1" " real" " 30 "
- Maximum value that J0 can obtain in fitting
-
-.BI "-chi1" " real" " 30 "
- Maximum value that Chi0 can obtain in fitting
-
-.BI "-w1" " real" " 1 "
- Maximum value that Radius can obtain in fitting
-
-.BI "-fc" " real" " 1 "
- Force constant in the penalty function for going outside the borders given with the above six options.
-
-.BI "-step" " real" " 0.01 "
- Step size in parameter optimization. Is used as a fraction of the starting value, should be less than 10%. At each reinit step the step size is updated.
-
-.BI "-elem" " string" " "
- List of elements to optimize, e.g. "H C Br". The other available elements in gentop.xml are left unmodified
-
-.BI "-seed" " int" " 1993"
- Random number seed for reinit
-
-.BI "-[no]random" "no "
- Generate completely random starting parameters within the limits set by the options. This will be done at the very first step only.
-
-.BI "-[no]zero" "yes "
- Use molecules with zero dipole in the fit as well
-
-.BI "-[no]weight" "yes "
- Perform a weighted fit, by using the errors in the dipoles presented in the input file. This may or may not improve convergence.
-
-.BI "-hfac" " real" " 0 "
- Fudge factor to scale the J00 of hydrogen by (1 + hfac * qH). Default hfac is 0, means no fudging.
-
-.BI "-[no]opthfac" "no "
- Optimize the fudge factor to scale the J00 of hydrogen (see above). If set, then
-.B -hfac
-set the absolute value of the largest hfac. Above this, a penalty is incurred.
-
-.BI "-slater_max" " int" " 6"
- Largest Slater function to be used when optimizing EEM props
-
+++ /dev/null
-.TH tune_pol 1 "Thu 16 Oct 2008"
-.SH NAME
-tune_pol
-.B VERSION 4.0_rc1
-.SH SYNOPSIS
-\f3tune_pol\fP
-.BI "-[no]h" ""
-.BI "-nice" " int "
-.SH DESCRIPTION
-tune_pol optimes group polarizabilities that together build
-an additive model for polarization.
-.SH OTHER OPTIONS
-.BI "-[no]h" "no "
- Print help info and quit
-
-.BI "-nice" " int" " 0"
- Set the nicelevel
-
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff