gmxgrompp (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. gmxgrompp also reads
parameters for gmxmdrun (eg. number of MD steps, time step, cut-off). Eventually a binary file is
produced that can serve as the sole input file for the MD program.
gmxgrompp 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.
gmxgrompp 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.
gmxgrompp 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 gmxconvert-tpr is
more convenient than gmxgrompp. You then supply the old checkpoint file directly to gmxmdrun with
-cpi. If you wish to change the ensemble or things like output frequency, then supplying the checkpoint
file to gmxgrompp 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 gmxmdrun-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 gmxgrompp has read. If in doubt, you can start gmxgrompp 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 files.
The -maxwarn option can be used to override warnings printed by gmxgrompp 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.
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