Difference between revisions of "Gromacs"
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''From the Gromacs web site:'' '''GROMACS''' is a versatile package to perform molecular dynamics and energy minimization, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers. GROMACS supports all the usual algorithms you expect from a modern molecular dynamics implementation, (check the online reference or manual for details), but there are also quite a few features that make it stand out from the competition. | ''From the Gromacs web site:'' '''GROMACS''' is a versatile package to perform molecular dynamics and energy minimization, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers. GROMACS supports all the usual algorithms you expect from a modern molecular dynamics implementation, (check the online reference or manual for details), but there are also quite a few features that make it stand out from the competition. | ||
{{AppStandardHeader|2016|gromacs}} | {{AppStandardHeader|2016.2|gromacs}} | ||
{{ | {{AppRunningOnAll}} | ||
=== Submitting Jobs === | === Submitting Jobs === | ||
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module add apps/gromacs/2016 | module add apps/gromacs/2016 | ||
mpirun -np $ | mpirun -np $SLURM_NTASKS gmx_mpi -v | ||
</pre> | </pre> | ||
<br> | <br> |
Latest revision as of 19:18, 3 December 2019
Description
From the Gromacs web site: GROMACS is a versatile package to perform molecular dynamics and energy minimization, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers. GROMACS supports all the usual algorithms you expect from a modern molecular dynamics implementation, (check the online reference or manual for details), but there are also quite a few features that make it stand out from the competition.
Version
- 2016.2
Authorized Users
CIRCE
account holdersRRA
account holdersSC
account holders
Platforms
CIRCE
clusterRRA
clusterSC
cluster
Modules
Gromacs requires the following module file to run:
apps/gromacs/2016.2
- See Modules for more information.
Running Gromacs on CIRCE/SC
The Gromacs user guide is essential to understanding the application and making the most of it. The guide and this page should help you to get started with your simulations. Please refer to the Documentation section for a link to the guide.
- Note on CIRCE: Make sure to run your jobs from your $WORK directory!
- Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.
Submitting Jobs
In order to start a simulation, you will need a protein or molecule to use. Go to http://www.rcsb.org/pdb/ and grab one in .pdb
format. Follow the below procedure for simple molecules.
- Run
pdb2gmx -f <pdb file>
file(s). - Run
editconf
with proper parameters to change the dimensions of the box. - Run
genbox
with proper parameters to add solvate. - Run
grompp
to pre-process your input data.
- An additional file is needed for
grompp
called `grommp.mdp`. You can grab a copy of it from /apps/gromacs/4.5.5/share/gromacs/tutor/methanol and modify it in your local directory as needed.
The script below (for testing, name it “gromacs-test.sh”) can be copied into your job directory (the folder with your input files) and modified so that you can submit batch processes to the queue. For help on submitting jobs to the queue, see our SLURM User’s Guide. Scripts are provided as examples only. Your SLURM executables, tools, and options will vary.
#!/bin/bash # #SBATCH --comment=gromacs-test #SBATCH --ntasks=16 #SBATCH --job-name=gromacs-test #SBATCH --output=output.%j.gromacs-test #SBATCH --time=01:00:00 #### SLURM 16 processor Gromacs test to run for 1 hour. module purge module add apps/gromacs/2016 mpirun -np $SLURM_NTASKS gmx_mpi -v
Next, you can change to your job’s directory, and run the sbatch command to submit the job:
[user@login0 ~]$ cd my/jobdir [user@login0 jobdir]$ sbatch ./gromacs-test.sh
- You can view the status of your job with the “squeue -u <username>” command
Documentation
Home Page, User Guides, and Manuals
- Gromacs Home Page
- Gromacs Manual
Benchmarks, Known Tests, Examples, Tutorials, and Other Resources
- GROMACS Tutorials
- /apps/gromacs/4.5.5/share/gromacs/tutor
- http://www.gromacs.org/Documentation/Tutorials
More Job Information
See the following for more detailed job submission information:
Reporting Bugs
Report bugs with Gromacs to the IT Help Desk: rc-help@usf.edu