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       grompp - makes a run input file

       VERSION 4.0.1


       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  -[no]h  -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 calls a preprocessor to resolve includes,  macros  etcetera.  By
       default   we  use  the  cpp  in  your  path.  To  specify  a  different
       macro-preprocessor (e.g. m4) or alternative location you can put a line
       in  your parameter file specifying the path to that program. Specifying
       -pp will get the pre-processed topology file written out.

       If your system does not  have  a  c-preprocessor,  you  can  still  use
       grompp,  but  you  do  not  have  access  to the features from the cpp.
       Command line options to the c-preprocessor can be given  in  the   .mdp
       file. See your local manual (man cpp).

       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.   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  have  exact  restarts  when  using  pressure and/or Nose-Hoover
       temperature coupling. For an exact restart do not forget  to  turn  off
       velocity generation and turn on unconstrained starting when constraints
       are present in the system.  If you want to continue a crashed  run,  it
       is easier to use  tpbconv.

       Using  the  -morse option grompp can convert the harmonic bonds in your
       topology to morse potentials. This makes it possible  to  break  bonds.
       For  this  option  to  work you need an extra file in your $GMXLIB with
       dissociation energy. Use the -debug option to get more  information  on
       the  workings  of  this  option  (look for MORSE in the grompp.log file
       using less or something like that).

       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 make notice 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).  Finally, you can see the
       contents of the run input file with the  gmxdump program.


       -f grompp.mdp Input, Opt.
        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 tpb tpa

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

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

       -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: edr ene


        Print help 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

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

        Renumber atomtypes and minimize number of atomtypes



       More      information     about     GROMACS     is     available     at

                                Thu 16 Oct 2008                      grompp(1)