GROMACS
Gromacs (http://www.gromacs.org) is available at the CAC in a parallel solver. At this time no visualization is available on Nyx or Flux. Gromacs is available in a single precision (recommended) and double precision for those who need it. All commands for a double precision run will be suffixed with _d. For example mdrun will become mdrun_d, grompp will become grompp_d, etc.
To use Gromacs, you need to first load the module.
module load gromacs
Here is a sample PBS file that will run Gromacs with 10 processors.
#### PBS preamble
#PBS -N gromacs_example
#PBS -M uniqname@umich.edu
#PBS -m abe
#PBS -l nodes=5:ppn=2,mem=1gb,walltime=100:00:00
#PBS -j oe
#PBS -V
#PBS -A example_flux
#PBS -l qos=flux
#PBS -q flux
#### End PBS preamble
# Include the next three lines always
if [ "x${PBS_NODEFILE}" != "x" ] ; then
cat $PBS_NODEFILE # contains a list of the CPUs you were using if run with PBS
fi
# Put your job commands after this line
# cd to your input directory first, assumed to be under your home dir
cd ${HOME}/gromacs/inputs
# run gromacs (mdrun or mdrun_d)
mpirun -np cpuS mdrun
Gromacs requires that inputs be prepped before ran. You can ether add these commands before your mpirun or you can run them (they take very little time) before you submit your job. The most important command is grompp.
grompp preps your input for a parallel run. For the best performance run grommp like so:
grompp
This will organize all the a large system for a parallel run.
trjconv -f traj.trr -o btraj.trr
Note, do not use parallel gromacs if simulating a single protein! This will run slower than a serial run (mpirun -np 1 mdrun). Speed-ups do exist for large single proteins on a single node with multiple CPUs but not for more than one node and multiple CPUs. In this case, request resources with something like
#PBS -l nodes=1:ppn=2,mem=1gb
and run on only 2 CPUs. Any more and your simulation will slow down, wasting your time and wasting resources. For more information look at the grommp man page. (man grompp)
For systems with any molecules or membrane systems Gromacs scales very well.
The following is a list of all Gromacs commands. Most are available in the _d version also. Some may not work; if you have questions email us at: hpc-support@umich.edu
anadock average completion.bash completion.csh completion.zsh editconf eneconv ffscan g_anaeig g_analyze g_angle g_bond g_bundle g_chi g_cluster g_clustsize g_confrms g_covar genbox genconf g_enemat g_energy genion genpr g_filter g_gyrate g_h2order g_hbond g_helix g_lie g_mdmat g_mindist g_morph g_msd gmxcheck gmxdump GMXRC GMXRC.bash GMXRC.csh GMXRC.zsh g_nmeig g_nmens g_nmtraj g_order g_potential g_rama g_rdf g_rms g_rmsdist g_rmsf grompp g_rotacf g_saltbr g_sas g_sgangle g_sham g_sorient g_tcaf g_traj g_velacc g_wham luck make_edi make_ndx mdrun mk_angndx pdb2gmx protonate tpbconv trjcat trjconv trjorder wheel x2top xpm2ps



