A simple example on how Gromacs maps forcefield parameters (OPLS) to a structure (methanol.gro)

Gromacs 5.0 or later version installed

From the command line run:

./run.sh

This scripts uses grompp to read the input files and generate a binary (.tpr) file, and it uses mdrun to run the MD simulation based on the generated tpr file.

Stored in output dir under the filename methNVE*

The simulation is setup to use the OPLS forcefield based on the gromacs template library (stored in gro_ff_tmplts/oplsaa.ff) and a user-defined template file (my_ff_tmplts/oplsaa.ff/methanol.itp).

• grompp cpp: C++ code for the gromacs preprocessor

• grompp h: header file for the gromacs preprocessor