Gromacs

From Biowerkzeug Wiki

Gromacs [1, 2, 3, 4] is a MD package developed in Groningen, Netherlands, which is published under the GNU Public license. It's claim to fame is

• raw speed (due to hand coded assembly inner loops and a few optimisations)
• extensive collection of analysis tools
• coded in C

Most force fields can be used, though it only comes natively with Gromos96 (ffG43, ffG53), OPLS-AA, Encad, and the deprecated Gromacs FF ("ffgmx" – don't use it!). The Charmm FF has also been ported.

Gromacs is fairly easy to install and for Macs it is contained in the Fink distribution.

Documentation

Gromacs comes with quite extensive documentation (accessible through their home page). Especially helpful are

• Online Reference manual
• Gromacs Wiki
• Mailinglist archives

Tutorials

• Gromacs tutorials
• Free energy calculations with Gromacs (from alchemistry.org)
• See also the share/tutor directory of the Gromacs distribution

References

1. H. J. C. Berendsen, D. van der Spoel, and R. van Drunen. GROMACS: A message-passing parallel molecular dynamics implementation. Comp. Phys. Comm., 91:43–56, 1995.

   [Berendsen1995]

2. Erik Lindahl, Berk Hess, and David van der Spoel. Gromacs 3.0: A package for molecular simulation and trajectory analysis. J. Mol. Mod., 7(8):306–317, 2001. doi:10.1007/s008940100045.

   [Lindahl2001]

3. Error fetching PMID 16211538: [vanderSpoel2005]
4. B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl. GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. J. Chem. Theo. Comp., 4(3):435–447, Feb 2008. doi:10.1021/ct700301q.

   [Hess2008]

5. Error fetching PMID 17405124: [Kutzner2007]