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.
See versions of gromacs which are available:
$ module avail gromacs
Load a particular version into your environment and run it:
$ module load gromacs/2018.2 $ gmx
Note: Please use the
-nt option to limit the number of threads launched by gmx to be the same amount as in your SLURM sbatch allocation. See the gromacs documentation for more information.
Notes from the sysadmin during installation:
$ cd /tmp $ wget http://ftp.gromacs.org/pub/gromacs/gromacs-2018.2.tar.gz $ tar xf gromacs-2018.2.tar.gz $ cd gromacs-2018.2 $ mkdir build $ cd build $ sudo yum install fftw-devel.x86_64 $ cmake3 .. -DCMAKE_INSTALL_PREFIX=/export/apps/gromacs/2018.2 $ make $ sudo mkdir -p /export/apps/gromacs/2018.2 $ sudo chown aorth /export/apps/gromacs/2018.2 $ make install $ sudo chown -R root:root /export/apps/gromacs/2018.2
Gromacs recommends sourcing the
GMXRC.bash script to set up the user's environment, but since we're using environment modules we can't do that. Instead, I compared the output
env before and after loading the
GMXRC.bash environment and then used that to create the module file.