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Information

Purpose: Molecular Dynamics
Latest version: 2018.1
License: GNU LGPL
Website: http://www.gromacs.org/

Gromacs is a program for general molecular dynamics, notable for its fast computation of 1-4 interactions.

It can implement regular molecular dynamics simulations using a variety of integrators, Langevin dynamics, energy minimisation, test-particle insertion, etc. It implements a variety of methods to calculate electrostatics and Van der Waals interactions, thermostats and barostats, 2- and 3-dimensional periodic boundary conditions, etc.

 

 

Benchmark

Gromacs 5.1.2 benchmark at collserola:

Actual speed-up (green) and ideal speed-up (blue) vs. number of cores for the NPT simulation of a protein with Amber force field, SPC water, PME electrostatics, no PME-dedicated node.

Note that, in runs with a large number of CPUs, performance can improve greatly by finding a correct balance between PME and particle threads in a problem-specific fashion. Here we show default behaviour, without custom optimisations.

 

 

SLURM Submit script example

For more information use the Job Script Generator.

For optimal performance, before a long production run, you are advised to experiment with different thread allocations to PME and DD tasks, using mdrun options. Please refer to the Gromacs documentation for more details.

 

 

Tutorial

You can follow this tutorial about simulation of a protein with Gromacs to get hands-on with the program.

 

 

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