Provided by: gromacs-data_4.6.5-1build1_all bug


       grompp - makes a run input file

       VERSION 4.6.5


       grompp  -f  grompp.mdp  -po mdout.mdp -c conf.gro -r conf.gro -rb conf.gro -n index.ndx -p -pp -o topol.tpr -t traj.trr -e ener.edr  -ref  rotref.trr  -[no]h
       -[no]version -nice int -[no]v -time real -[no]rmvsbds -maxwarn int -[no]zero -[no]renum


       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.   grompp also reads parameters for the  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.

        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.

         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 can be supplied with  -r,
       otherwise restraining will be done with respect to the conformation from the   -c  option.
       For  free  energy  calculation the the 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.

        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  tpbconv is more convenient than  grompp.  You then supply the old checkpoint
       file  directly  to   mdrun  with   -cpi. If you wish to change the ensemble or things like
       output frequency, then supplying the checkpoint file to  grompp with  -t along with a  new
       .mdp file with  -f 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 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  grompp has read. If  in  doubt,  you  can  start
       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  gmxdump program.  gmxcheck can be used to compare the contents of two run input

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


       -f grompp.mdp Input
        grompp input file with MD parameters

       -po mdout.mdp Output
        grompp input file with MD parameters

       -c conf.gro Input
        Structure file: gro g96 pdb tpr etc.

       -r conf.gro Input, Opt.
        Structure file: gro g96 pdb tpr etc.

       -rb conf.gro Input, Opt.
        Structure file: gro g96 pdb tpr etc.

       -n index.ndx Input, Opt.
        Index file

       -p Input
        Topology file

       -pp Output, Opt.
        Topology file

       -o topol.tpr Output
        Run input file: tpr tpb tpa

       -t traj.trr Input, Opt.
        Full precision trajectory: trr trj cpt

       -e ener.edr Input, Opt.
        Energy file

       -ref rotref.trr In/Out, Opt.
        Full precision trajectory: trr trj cpt


        Print help info and quit

        Print version info and quit

       -nice int 0
        Set the nicelevel

        Be loud and noisy

       -time real -1
        Take frame at or first after this time.

        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

        Set parameters for bonded interactions without defaults to zero instead of generating  an

        Renumber atomtypes and minimize number of atomtypes



       More information about GROMACS is available at <>.

                                          Mon 2 Dec 2013                                grompp(1)