Provided by: gromacs-data_2019.1-1_all bug


       gmx-grompp - Make a run input file


          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]


       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
          #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

       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

       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 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>] (
              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>] ( (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



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       2019, GROMACS development team