grompp

From wiki.gromacs.org

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 .tpr file is produced that can serve as the sole input file for the MD program.

grompp works by running another pre-processor (described in Include File Mechanism), and if you choose to make use of the define run parameter you need to get the syntax right. For example, define = -DMPC_POSRES has an outcome different from define = -DDMPC_POSRES.

[edit] Parallel calculations

Note that in order to run a parallel calculation over xxx processes, the -np xxx flag to grompp must be used in concert with a correctly configured MPI environment, a suitable mpirun command before mdrun_mpi -np xxx (or whatever your installation process used as an MPI suffix), and all relevant files visible to the master MPI process. No other GROMACS program is MPI-aware, so do not feel you need to use (or even build) grompp_mpi etc.