Difference between revisions of "Gromacs"

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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.
===Serial===
 
* intel
 
* {{#lowercase:{{#var:app}}}}
 
 
===Parallel (MPI)===
 
===Parallel (MPI)===
* intel
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* intel/2016.0.109
* openmpi
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* openmpi/1.10.2
 
* {{#lowercase:{{#var:app}}}}
 
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{{#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.

Revision as of 18:31, 1 August 2016

Description

Gromacs website  

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
  • {{#lowercase:Gromacs}}

System Variables

  • HPC_GROMACS_DIR - installation directory
  • HPC_GROMACS_BIN - executable directory
  • HPC_GROMACS_INC - header file directory
  • HPC_GROMACS_LIB - library directory


PBS Script Examples

See the Gromacs_PBS page for Gromacs PBS 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)