GROMACS

Gromacs (http://gromacs.org) is available at the CAC in a parallel solver. At this time no visualization is available at the CAC. 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 sufixed with _d. For example mdrun will become mdrun_d, grompp will become grompp_d, etc.

To use Gromacs run:

module load gromacs

A sample PBS file follows:

#!/bin/sh #PBS -N gromacs #PBS -l nodes=5:ppn=2,walltime=100:00:00 #PBS -M uniquename@umich.edu #PBS -m bae #PBS -j oe #PBS -V echo "i ran on:" cat $PBS_NODEFILE #move to input cd ~/gromacs/inputs/ #run gromacs (mdrun or mdrun_d) mpirun -np CPUS mdrun

Gromacs requires that inputs be preped 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 -sort -shuffle -np 10 (if going to run on 10 cpus)

This will organize all the a large system for a parallel run.

When using -shuffle the trajectory will need to deshuffled when the run is compleated.

trjconv -f traj.trr -n deshuf -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 in a single node with multiple cpus but not for more than one node multiple cpus. In this case request resources like:

#PBS -l nodes=1:ppn=2

and run on only 2 cpus. Any more and your simulation will slow 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: cac-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



About the CAC Academics Getting Started Getting Help FAQ Resources Current Outages No outages have been reported Planned Outages No outages have been scheduled Search The CAC	GROMACS Gromacs (http://gromacs.org) is available at the CAC in a parallel solver. At this time no visualization is available at the CAC. 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 sufixed with `_d`. For example `mdrun` will become `mdrun_d`, `grompp` will become `grompp_d`, etc. To use Gromacs run: `module load gromacs` A sample PBS file follows: `#!/bin/sh #PBS -N gromacs #PBS -l nodes=5:ppn=2,walltime=100:00:00 #PBS -M uniquename@umich.edu #PBS -m bae #PBS -j oe #PBS -V echo "i ran on:" cat $PBS_NODEFILE #move to input cd ~/gromacs/inputs/ #run gromacs (mdrun or mdrun_d) mpirun -np CPUS mdrun` Gromacs requires that inputs be preped 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 -sort -shuffle -np 10 (if going to run on 10 cpus)` This will organize all the a large system for a parallel run. When using `-shuffle` the trajectory will need to deshuffled when the run is compleated. `trjconv -f traj.trr -n deshuf -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 in a single node with multiple cpus but not for more than one node multiple cpus. In this case request resources like: `#PBS -l nodes=1:ppn=2` and run on only 2 cpus. Any more and your simulation will slow 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: cac-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