NAME

       gmx-grompp - Make a run input file

SYNOPSIS

          gmx grompp [-f [<.mdp>]] [-c [<.gro/.g96/...>]] [-r [<.gro/.g96/...>]]
                     [-rb [<.gro/.g96/...>]] [-n [<.ndx>]] [-p [<.top>]]
                     [-t [<.trr/.cpt/...>]] [-e [<.edr>]]
                     [-ref [<.trr/.cpt/...>]] [-po [<.mdp>]] [-pp [<.top>]]
                     [-o [<.tpr>]] [-imd [<.gro>]] [-[no]v] [-time <real>]
                     [-[no]rmvsbds] [-maxwarn <int>] [-[no]zero] [-[no]renum]

DESCRIPTION

       gmx  grompp  (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.   gmx  grompp  also  reads
       parameters  for  gmx  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.

       gmx  grompp uses the atom names from the topology file. The atom names in the coordinate file (option -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.

       gmx grompp 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 .mdp file:

          define = -DVARIABLE1 -DVARIABLE2
          include = -I/home/john/doe

       For further information a C-programming textbook may help you out.  Specifying the -pp 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 must be supplied with -r (can be the
       same file as supplied for -c). For free energy calculations, separate reference  coordinates  for  the  B
       topology can be supplied with -rb, otherwise they will be equal to those of the A topology.

       Starting coordinates can be read from trajectory with -t.  The last frame with coordinates and velocities
       will be read, unless the -time option is used. Only if this information is absent will the coordinates in
       the  -c  file be used.  Note that these velocities will not be used when gen_vel = yes in your .mdp file.
       An energy file can be supplied with -e to read Nose-Hoover and/or Parrinello-Rahman coupling variables.

       gmx grompp can be used to restart simulations (preserving continuity) by supplying just a checkpoint file
       with  -t.  However, for simply changing the number of run steps to extend a run, using gmx convert-tpr is
       more convenient than gmx grompp.  You then supply the old checkpoint file  directly  to  gmx  mdrun  with
       -cpi.  If  you wish to change the ensemble or things like output frequency, then supplying the checkpoint
       file to gmx grompp with -t along with a new .mdp file with -f  is  the  recommended  procedure.  Actually
       preserving the ensemble (if possible) still requires passing the checkpoint file to gmx mdrun -cpi.

       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 -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  take  note  of all warnings on the screen, and correct where
       necessary. Do also look at the contents of the mdout.mdp file; this contains comment lines,  as  well  as
       the  input  that  gmx grompp has read. If in doubt, you can start gmx grompp with the -debug option which
       will give you more information in a file called grompp.log (along with real debug info). You can see  the
       contents  of  the run input file with the gmx dump program. gmx check can be used to compare the contents
       of two run input files.

       The -maxwarn option can be used to override warnings printed by gmx grompp 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.

OPTIONS

       Options to specify input files:

       -f [<.mdp>] (grompp.mdp)
              grompp input file with MD parameters

       -c [<.gro/.g96/...>] (conf.gro)
              Structure file: gro g96 pdb brk ent esp tpr

       -r [<.gro/.g96/...>] (restraint.gro) (Optional)
              Structure file: gro g96 pdb brk ent esp tpr

       -rb [<.gro/.g96/...>] (restraint.gro) (Optional)
              Structure file: gro g96 pdb brk ent esp tpr

       -n [<.ndx>] (index.ndx) (Optional)
              Index file

       -p [<.top>] (topol.top)
              Topology file

       -t [<.trr/.cpt/...>] (traj.trr) (Optional)
              Full precision trajectory: trr cpt tng

       -e [<.edr>] (ener.edr) (Optional)
              Energy file

       Options to specify input/output files:

       -ref [<.trr/.cpt/...>] (rotref.trr) (Optional)
              Full precision trajectory: trr cpt tng

       Options to specify output files:

       -po [<.mdp>] (mdout.mdp)
              grompp input file with MD parameters

       -pp [<.top>] (processed.top) (Optional)
              Topology file

       -o [<.tpr>] (topol.tpr)
              Portable xdr run input file

       -imd [<.gro>] (imdgroup.gro) (Optional)
              Coordinate file in Gromos-87 format

       Other options:

       -[no]v (no)
              Be loud and noisy

       -time <real> (-1)
              Take frame at or first after this time.

       -[no]rmvsbds (yes)
              Remove constant bonded interactions with virtual sites

       -maxwarn <int> (0)
              Number of allowed warnings during input processing. Not for normal use and may  generate  unstable
              systems

       -[no]zero (no)
              Set parameters for bonded interactions without defaults to zero instead of generating an error

       -[no]renum (yes)
              Renumber atomtypes and minimize number of atomtypes

SEE ALSO

       gmx(1)

       More information about GROMACS is available at <http://www.gromacs.org/>.

COPYRIGHT

       2020, GROMACS development team