Gromacs

Versatile package to perform molecular dynamics

Description

Gromacs is an engine to perform molecular dynamics simulations and energy minimization particularly for proteins. However, it can be used to model polymers, membranes and e.g. coarse grained systems. It also comes with plenty of analysis scripts.

Usage

To start working with Gromacs in Louhi, Murska, Vuori or Hippu use the module command:

module load gromacs/version

Omitting version will initialise the default version which will change when bugs are fixed or new versions are accepted stable. Vuori also has a double precision version of all executables (module 4.0.X.d).

Hippu is suitable for interactive use (preparation, analysis) and serial jobs. Murska and Vuori are recommended for serial jobs and normal parallel jobs. Louhi is intended for large jobs. Parallellisation parameters have a significant impact on scaling in (dd and npme).

Examples

The batch submission is different on all machines. Please consult the server manuals or the examples below:

Examples of Gromacs 4 jobs on Louhi.
Examples of Gromacs 3 and 4 jobs on Murska.
Examples of Gromacs 4 jobs on Vuori.
Examples of Gromacs 4 GPGPU-jobs on Vuori.

Other versions

You can check for other versions with the command module avail

After initialisation you can check, e.g. with

which mdrun

which shows where the code lives and hints how to modify the batch script initialisation.

Visualising trajectories

In addition to ngmx program in Gromacs, trajectory files can be visualized with the following programs:

• PyMOL molecular modeling system.
• VMD visualizing program for large biomolecular systems.

Visualising XY-plots

Gromacs tools produce output files made for the Grace program. These data can be visualized with program Grace. To start working with Grace, issue the command:

 module load grace

To plot all energy components in the energy.xvg file give:

 xmgrace -nxy energy.xvg

Examples and links

• My first Gromacs simulation - simple input example (Murska)
  
• More examples in $GMXDATA/gromacs/tutor/
• Gromacs Worskhop 2007 at CSC lectures and exercises
• The Dundee PRODRG Server for converting coordinates for small molecules to the Gromacs coordinate (only .gro format available) and topology formats.
• HOW-TOs at the Gromacs web site
  

Citation

Please use the following citation when publishing results obtained with Gromacs 3.x:

* GROMACS: A message-passing parallel molecular dynamics implementation
  H.J.C. Berendsen, D. van der Spoel and R. van Drunen
  Comp. Phys. Comm. 91, 43-56 (1995)
 
* GROMACS 3.0: A package for molecular simulation and trajectory analysis
  Erik Lindahl, Berk Hess and David van der Spoel
  J. Mol. Mod. 7, 306-317 (2001)

For version 4 please cite the following paper:

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) 

Manuals and further info

• Gromacs developers www-pages
• Coarse Graining examples
  
• Other workshop material at CSC
  
• A very useful Gromacs Users Mailing list
  

Please contact helpdesk@csc.fi more information.