.TH grompp 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME grompp - makes a run input file .B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3grompp\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 "\-[no]version" "" .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. \&\fB grompp\fR also reads parameters for the \fB mdrun\fR \&(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. \&\fB grompp\fR uses the atom names from the topology file. The atom names \&in the coordinate file (option \fB \-c\fR) 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. \&\fB grompp\fR uses a built\-in preprocessor to resolve includes, macros, \&etc. The preprocessor supports the following keywords: \&ifdef VARIABLE \&ifndef VARIABLE \&else \&endif \&define VARIABLE \&undef VARIABLE include "filename" \&include filename \&The functioning of these statements in your topology may be modulated by \&using the following two flags in your \fB .mdp\fR file: \&\fB define = \-DVARIABLE1 \-DVARIABLE2 \&include = \-I/home/john/doe\fR \&For further information a C\-programming textbook may help you out. \&Specifying the \fB \-pp\fR flag will get the pre\-processed \&topology file written out so that you can verify its contents. \&When using position restraints a file with restraint coordinates \&can be supplied with \fB \-r\fR, otherwise restraining will be done \&with respect to the conformation from the \fB \-c\fR option. \&For free energy calculation the the coordinates for the B topology \&can be supplied with \fB \-rb\fR, otherwise they will be equal to \&those of the A topology. \&Starting coordinates can be read from trajectory with \fB \-t\fR. \&The last frame with coordinates and velocities will be read, \&unless the \fB \-time\fR option is used. Only if this information \&is absent will the coordinates in the \fB \-c\fR file be used. \&Note that these velocities will not be used when \fB gen_vel = yes\fR \&in your \fB .mdp\fR file. An energy file can be supplied with \&\fB \-e\fR to read Nose\-Hoover and/or Parrinello\-Rahman coupling \&variables. \&\fB grompp\fR can be used to restart simulations (preserving \&continuity) by supplying just a checkpoint file with \fB \-t\fR. \&However, for simply changing the number of run steps to extend \&a run, using \fB tpbconv\fR is more convenient than \fB grompp\fR. \&You then supply the old checkpoint file directly to \fB mdrun\fR \&with \fB \-cpi\fR. If you wish to change the ensemble or things \&like output frequency, then supplying the checkpoint file to \&\fB grompp\fR with \fB \-t\fR along with a new \fB .mdp\fR file \&with \fB \-f\fR is the recommended procedure. \&By default, all bonded interactions which have constant energy due to \&virtual site constructions will be removed. If this constant energy is \¬ zero, this will result in a shift in the total energy. All bonded \&interactions can be kept by turning off \fB \-rmvsbds\fR. 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 take note of all warnings \&on the screen, and correct where necessary. Do also look at the contents \&of the \fB mdout.mdp\fR file; this contains comment lines, as well as \&the input that \fB grompp\fR has read. If in doubt, you can start \fB grompp\fR \&with the \fB \-debug\fR option which will give you more information \&in a file called \fB grompp.log\fR (along with real debug info). You \&can see the contents of the run input file with the \fB gmxdump\fR \&program. \fB gmxcheck\fR can be used to compare the contents of two \&run input files. The \fB \-maxwarn\fR option can be used to override warnings printed \&by \fB grompp\fR that otherwise halt output. In some cases, warnings are \&harmless, but usually they are not. The user is advised to carefully \&interpret the output messages before attempting to bypass them with \&this option. .SH FILES .BI "\-f" " grompp.mdp" .B Input grompp input file with MD parameters .BI "\-po" " mdout.mdp" .B Output grompp input file with MD parameters .BI "\-c" " conf.gro" .B Input Structure file: gro g96 pdb tpr etc. .BI "\-r" " conf.gro" .B Input, Opt. Structure file: gro g96 pdb tpr etc. .BI "\-rb" " conf.gro" .B Input, Opt. Structure file: gro g96 pdb tpr etc. .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 Run input file: tpr tpb tpa .BI "\-t" " traj.trr" .B Input, Opt. Full precision trajectory: trr trj cpt .BI "\-e" " ener.edr" .B Input, Opt. Energy file .SH OTHER OPTIONS .BI "\-[no]h" "no " Print help info and quit .BI "\-[no]version" "no " Print version info and quit .BI "\-nice" " int" " 0" Set the nicelevel .BI "\-[no]v" "no " 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. Not for normal use and may generate unstable systems .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 .SH SEE ALSO .BR gromacs(7) More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.