Difference between revisions of "Gromacs"
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<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | ||
|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
| − | |{{#vardefine:exe| | + | |{{#vardefine:exe|}} <!--ADDITIONAL INFO--> |
|{{#vardefine:pbs|1}} <!--PBS SCRIPTS--> | |{{#vardefine:pbs|1}} <!--PBS SCRIPTS--> | ||
|{{#vardefine:policy|}} <!--POLICY--> | |{{#vardefine:policy|}} <!--POLICY--> | ||
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==Required Modules== | ==Required Modules== | ||
You must load the appropriate modules in your submission script. | You must load the appropriate modules in your submission script. | ||
| − | |||
| − | |||
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===Parallel (MPI)=== | ===Parallel (MPI)=== | ||
| − | * intel | + | * intel/2016.0.109 |
| − | * openmpi | + | * openmpi/1.10.2 |
| − | * {{ | + | * {{lc:{{#var:app}}}} |
==System Variables== | ==System Variables== | ||
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<!--Run--> | <!--Run--> | ||
{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
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===GPU Support=== | ===GPU Support=== | ||
Gromacs 4.6.5 was built with CUDA-based GPU acceleration in both serial and parallel (MPI+OpenMP) executables. It is not necessary to load the CUDA module. It will be loaded by the Gromacs 4.6.5 module. If no GPUs are available, Gromacs 4.6.5 will note that no GPUs were found and will run without them. | Gromacs 4.6.5 was built with CUDA-based GPU acceleration in both serial and parallel (MPI+OpenMP) executables. It is not necessary to load the CUDA module. It will be loaded by the Gromacs 4.6.5 module. If no GPUs are available, Gromacs 4.6.5 will note that no GPUs were found and will run without them. | ||
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|}} | |}} | ||
| − | <!-- | + | <!--SLURM scripts--> |
| − | {{#if: {{#var: pbs}}|== | + | {{#if: {{#var: pbs}}|==Job Script Examples== |
| − | See the [[{{PAGENAME}} | + | See the [[{{PAGENAME}}_Job_Scripts]] page for {{#var: app}} Job script examples. |
|}} | |}} | ||
<!--Policy--> | <!--Policy--> | ||
Latest revision as of 21:31, 6 December 2019
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.
Required Modules
You must load the appropriate modules in your submission script.
Parallel (MPI)
- intel/2016.0.109
- openmpi/1.10.2
- gromacs
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
See the Gromacs_Job_Scripts page for Gromacs Job script examples.
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)
