Difference between revisions of "GROMACS"
Jump to navigation
Jump to search
(Created page with "Category:SoftwareCategory:Computational ChemistryCategory:Molecular Dynamics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|gromacs}} |{{#vardefine:url|http://...") |
|||
| (2 intermediate revisions by 2 users not shown) | |||
| Line 1: | Line 1: | ||
| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Chemistry]][[Category:Molecular Dynamics]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|gromacs}} | |{{#vardefine:app|gromacs}} | ||
| Line 6: | Line 6: | ||
|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
|{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | |{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | ||
| − | |{{#vardefine:job|}} <!--JOB SCRIPTS--> | + | |{{#vardefine:job|1}} <!--JOB SCRIPTS--> |
|{{#vardefine:policy|}} <!--POLICY--> | |{{#vardefine:policy|}} <!--POLICY--> | ||
|{{#vardefine:testing|}} <!--PROFILING--> | |{{#vardefine:testing|}} <!--PROFILING--> | ||
|{{#vardefine:faq|}} <!--FAQ--> | |{{#vardefine:faq|}} <!--FAQ--> | ||
| − | |{{#vardefine:citation|}} <!--CITATION--> | + | |{{#vardefine:citation|1}} <!--CITATION--> |
|{{#vardefine:installation|}} <!--INSTALLATION--> | |{{#vardefine:installation|}} <!--INSTALLATION--> | ||
|} | |} | ||
| Line 26: | Line 26: | ||
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | ||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_INC - header file directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_LIB - library directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
| Line 42: | Line 42: | ||
<!--Job Scripts--> | <!--Job Scripts--> | ||
{{#if: {{#var: job}}|==Job Script Examples== | {{#if: {{#var: job}}|==Job Script Examples== | ||
| − | + | ;Note: Use 'module spider gromacs' to find available gromacs versions. The module loads below may be outdated. | |
| + | <div class="mw-collapsible mw-collapsed" style="width:70%; padding: 5px; border: 1px solid gray;"> | ||
| + | ''Expand to view sample Parallel MPI script.'' | ||
| + | <div class="mw-collapsible-content" style="padding: 5px;"> | ||
| + | <pre> | ||
| + | #!/bin/bash | ||
| + | #SBATCH --job-name=gromacs | ||
| + | #SBATCH --mail-user=YOUR_MAIL_ADDRESS_HERE | ||
| + | #SBATCH --mail-type=FAIL,BEGIN,END | ||
| + | #SBATCH --output=gmx-%j.out | ||
| + | #SBATCH --ntasks=2 | ||
| + | #SBATCH --cpus-per-task=4 | ||
| + | #SBATCH --ntasks-per-socket=1 | ||
| + | #SBATCH --distribution=cyclic:block | ||
| + | #SBATCH --time=24:00:00 | ||
| + | #SBATCH --mem-per-cpu=1gb | ||
| + | |||
| + | module purge | ||
| + | ml gcc/8.2.0 openmpi/4.0.1 gromacs/2019.2 | ||
| + | |||
| + | export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK | ||
| + | srun --mpi=pmix_v3 gmx mdrun -ntomp ${SLURM_CPUS_PER_TASK} -s topol.tpr | ||
| + | </pre> | ||
| + | </div> | ||
| + | </div> | ||
| + | |||
| + | <div class="mw-collapsible mw-collapsed" style="width:70%; padding: 5px; border: 1px solid gray;"> | ||
| + | ''Expand to view sample GPU Acceleration script.'' | ||
| + | <div class="mw-collapsible-content" style="padding: 5px;"> | ||
| + | <pre> | ||
| + | #!/bin/bash | ||
| + | #SBATCH --job-name=multi-gpu | ||
| + | #SBATCH --mail-user=YOUR_MAIL_ADDRESS_HERE | ||
| + | #SBATCH --mail-type=FAIL,BEGIN,END | ||
| + | #SBATCH --output=gromacs_%j.log | ||
| + | #SBATCH --nodes=1 | ||
| + | #SBATCH --ntasks=2 | ||
| + | #SBATCH --tasks-per-node=2 | ||
| + | #SBATCH --cpus-per-task=7 | ||
| + | #SBATCH --ntasks-per-socket=1 | ||
| + | #SBATCH --distribution=cyclic:block | ||
| + | #SBATCH --time=2:00:00 | ||
| + | #SBATCH --mem-per-cpu=1gb | ||
| + | #SBATCH --partition=hpg2-gpu | ||
| + | #SBATCH --gres=gpu:a100:2 | ||
| + | |||
| + | module load gcc/5.2.0 openmpi/1.10.2 gromacs/2016.3-CUDA | ||
| + | |||
| + | export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK | ||
| + | srun --mpi=pmi2 --accel-bind=g --ntasks=$SLURM_NTASKS gmx mdrun -v | ||
| + | |||
| + | </pre> | ||
| + | </div> | ||
| + | </div> | ||
|}} | |}} | ||
<!--Policy--> | <!--Policy--> | ||
| Line 61: | Line 114: | ||
<!--Citation--> | <!--Citation--> | ||
{{#if: {{#var: citation}}|==Citation== | {{#if: {{#var: citation}}|==Citation== | ||
| − | If you publish research that uses {{#var:app}} you have to cite it as follows: | + | If you publish research that uses {{#var:app}} you have to cite it as follows:<br/> |
| − | + | GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation | |
| − | + | Hess, B., Kutzner, C., van der Spoel, D. and Lindahl, E. | |
| − | + | J. Chem. Theory Comput., 4, 435-447 (2008) | |
|}} | |}} | ||
<!--Installation--> | <!--Installation--> | ||
Latest revision as of 19:16, 5 January 2023
Description
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.
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.
Environment Modules
Run module spider gromacs to find out what environment modules are available for this application.
System Variables
- HPC_GROMACS_DIR - installation directory
- HPC_GROMACS_BIN - executable directory
- HPC_GROMACS_INC - header file directory
- HPC_GROMACS_LIB - library directory
Job Script Examples
- Note
- Use 'module spider gromacs' to find available gromacs versions. The module loads below may be outdated.
Expand to view sample Parallel MPI script.
#!/bin/bash
#SBATCH --job-name=gromacs
#SBATCH --mail-user=YOUR_MAIL_ADDRESS_HERE
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --output=gmx-%j.out
#SBATCH --ntasks=2
#SBATCH --cpus-per-task=4
#SBATCH --ntasks-per-socket=1
#SBATCH --distribution=cyclic:block
#SBATCH --time=24:00:00
#SBATCH --mem-per-cpu=1gb
module purge
ml gcc/8.2.0 openmpi/4.0.1 gromacs/2019.2
export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
srun --mpi=pmix_v3 gmx mdrun -ntomp ${SLURM_CPUS_PER_TASK} -s topol.tpr
Expand to view sample GPU Acceleration script.
#!/bin/bash #SBATCH --job-name=multi-gpu #SBATCH --mail-user=YOUR_MAIL_ADDRESS_HERE #SBATCH --mail-type=FAIL,BEGIN,END #SBATCH --output=gromacs_%j.log #SBATCH --nodes=1 #SBATCH --ntasks=2 #SBATCH --tasks-per-node=2 #SBATCH --cpus-per-task=7 #SBATCH --ntasks-per-socket=1 #SBATCH --distribution=cyclic:block #SBATCH --time=2:00:00 #SBATCH --mem-per-cpu=1gb #SBATCH --partition=hpg2-gpu #SBATCH --gres=gpu:a100:2 module load gcc/5.2.0 openmpi/1.10.2 gromacs/2016.3-CUDA export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK srun --mpi=pmi2 --accel-bind=g --ntasks=$SLURM_NTASKS gmx mdrun -v
Citation
If you publish research that uses gromacs you have to cite it as follows:
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
Hess, B., Kutzner, C., van der Spoel, D. and Lindahl, E.
J. Chem. Theory Comput., 4, 435-447 (2008)