ILRI Research Computing

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====== Gromacs ======
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.

===== Information =====

  * Version: 2018.2
  * Added: July, 2018
  * Link: http://www.gromacs.org/

===== Usage =====

See versions of gromacs which are available:
<code>$ module avail gromacs</code>

Load a particular version into your environment and run it:

<code>$ module load gromacs/2018.2
$ gmx</code>

**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 [[http://manual.gromacs.org/2018-current/user-guide/mdrun-performance.html#running-mdrun-within-a-single-node|gromacs documentation for more information]]. 

===== Installation ======
Notes from the sysadmin during installation:

<code>$ 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</code>

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.