GROMACS stands for Great Red Owns Many ACres of Sand. It is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

Below is a list of prerequisites for using GROMACS:

• Pathscale Compiler
• ACML
• FFTW3

Below is a list of additional prerequisites for using GROMACS with MPI support:

• OpenMPI

We support the following versions of GROMACS:

• GROMACS 3.3.3 (without MPI)
• GROMACS 3.3.3 (with MPI)

The default version of GCC will be loaded automatically. To load the different versions first determine which version you want to use.

For serial jobs:

module load compilers/pathscale-3.2 \
            math/fftw-3.1.2 \
            blas/acml-4.1.0-pathscale \
            md/gromacs-3.3.3

For MPI jobs:

module load compilers/pathscale-3.2 \
            math/fftw-3.1.2 \
            blas/acml-4.1.0-pathscale \
            mpi/openmpi-1.2.6-pathscale-3.2
            md/gromacs-3.3.3-openmpi-1.2.6

To use the command line completion aspects of your shell you can run the following (depending on your shell):

# for bash:
source `which completion.bash`
# for csh and tcsh:
source `which completion.csh`
# for zsh:
source `which completion.zsh`

We built GROMACS using the following options.

The process for building v3.3.3 is slightly different for MPI-enabled GROMACS and GROMACS without MPI support. The first two steps are different but the rest of the build and install process is the same.

First the following modules should be loaded:

$ module load compilers/pathscale-3.2 \
            math/fftw-3.1.2 \
            blas/acml-4.1.0-pathscale

Then run the following configure command:

$ ./configure CC=pathcc \
              CXX=pathCC \
              F77=pathf90 \
              CFLAGS="-O3 -OPT:Ofast -L/share/apps/fftw-3.1.2/lib -L/share/apps/acml-4.1.0/pathscale64/lib" \
              LIBS=-lacml \
              CPPFLAGS=-I/share/apps/fftw-3.1.2/include \
             --prefix=/share/apps/gromacs-3.3.3 \
             --with-fft=fftw3 \
             --with-pic \
             --with-external-lapack \
             --with-external-blas

First load the following modules:

$ module load compilers/pathscale-3.2 \
            math/fftw-3.1.2 \
            blas/acml-4.1.0-pathscale \
            mpi/openmpi-1.2.6-pathscale-3.2

Then run the following configure command:

$ ./configure CC=pathcc \
              CXX=pathCC \
              F77=pathf90 \
              CFLAGS="-O3 -OPT:Ofast -L/share/apps/fftw-3.1.2/lib -L/share/apps/acml-4.1.0/pathscale64/lib" \
              LIBS=-lacml \
              CPPFLAGS=-I/share/apps/fftw-3.1.2/include \
             --prefix=/share/apps/gromacs-3.3.3 \
             --with-fft=fftw3 \
             --with-pic \
             --with-external-lapack \
             --with-external-blas \
             --enable-mpi

Then build, test, and install the binaries and documentation.

$ make
$ make mdrun
$ sudo make install
$ sudo make install-mdrun
$ wget ftp://ftp.gromacs.org/pub/tests/gmxtest-3.3.3.tgz
$ tar zxf gmxtest-3.3.3.tgz
$ make tests
All 16 simple tests PASSED
FAILED. Check files in dec+water
1 out of 14 complex tests FAILED
All 63 kernel tests PASSED
All 45 pdb2gmx tests PASSED
$

Note: the failed dec+water test is normal see this page.

There is documentation for GROMACS on their website as well as in man pages (once you load the GROMACS module). There also appears to be some documentation and tutorials in the $GMXHOME/share/gromacs directory.