GROMACS

Description

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.  (From gromacs.org)

How to Access GROMACS

NERSC uses modules to manage access to software. To use the default version of GROMACS, type:

% module load gromacs

Using GROMACS on Franklin and Hopper

There are two ways of running gromacs on Franklin and Hopper: submitting a batch job, or running interactively in an interactive batch session.

Sample Batch Script for GROMACS on Franklin and Hopper

#PBS -N myjob 
#PBS -q debug
#PBS -l mppwidth=16
#PBS -l walltime=00:30:00
#PBS -j oe
#PBS -V 

cd $PBS_O_WORKDIR
module load gromacs 

aprun -n 16 mdrun_mpi >& test.log 

Then submit the job script using the qsub command, e.g., assuming the job script name is test_gromacs.pbs:

% qsub  test_gromacs.pbs 

Sample Interactive Batch Script for GROMACS on Franklin and Hopper

To request an interactive batch session, issue the command (e.g., requesting 8 PEs):

% qsub  -I -V -q interactive -l mppwidth=8 

When the batch session is returned to you, issue the following commands:

%  cd  $PBS_O_WORKDIR  
%  module load  gromacs   
%  aprun  -n 16 mdrun_mpi >& test.log

Using GROMACS on Carver

A sample batch script for Carver:

#PBS -l nodes=2:ppn=8,walltime=0:30:00
#PBS -N test
#PBS -j oe 
#PBS -q debug
#PBS -V
cd $PBS_O_WORKDIR 
module load gromacs 
mpirun -np 16 mdrun_mpi >& test.log

Documentation

Gromacs Documentaion

Compilation Instructions

Some advanced users may be interested in tweaking the GROMACS build parameters and building GROMACS themselves in their own directory. In order to aid in this process, and to provide a greater degree of transparency, the build instructions for the GROMACS module are listed below. The following procedure was used to build GROMACS on Hopper.

% module swap PrgEnv-pgi PrgEnv-gnu
% module swap gcc gcc/4.5.2
% ./configure --prefix=`pwd`/.. CC=cc CPP=cpp CXXCPP=cpp CXX=CC CPPFLAGS="-I/opt/fftw/3.2.2.1/include" CFLAGS="-fomit-frame-pointer -finline-functions -funroll-all-loops -O3" --program-suffix=_mpi LIBS="-L/opt/fftw/3.2.2.1/lib -lfftw3f -lm -lsci_gnu_mp" --enable-all-static --enable-mpi --without-x --without-xml --with-external-blas=yes --with-external-lapack=yes
% make
% make install

Availability