Gromacs: Difference between revisions
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== References == | == References == | ||
<biblio> | <biblio> | ||
#Berendsen1995 H. J. C. Berendsen, D. van der Spoel, and R. van Drunen. <i>GROMACS: A message-passing parallel molecular dynamics implementation.</i> Comp. Phys. Comm., 91:43–56, 1995 | #Berendsen1995 H. J. C. Berendsen, D. van der Spoel, and R. van Drunen. <i>GROMACS: A message-passing parallel molecular dynamics implementation.</i> Comp. Phys. Comm., 91:43–56, 1995. | ||
#Lindahl2001 Erik Lindahl, Berk Hess, and David van der Spoel. <i>Gromacs 3.0: A package for molecular simulation and trajectory analysis.</i> J. Mol. Mod., 7(8):306–317, 2001. doi:[http://dx.doi.org/10.1007/s008940100045 10.1007/s008940100045]. | #Lindahl2001 Erik Lindahl, Berk Hess, and David van der Spoel. <i>Gromacs 3.0: A package for molecular simulation and trajectory analysis.</i> J. Mol. Mod., 7(8):306–317, 2001. doi:[http://dx.doi.org/10.1007/s008940100045 10.1007/s008940100045]. | ||
#vanderSpoel2005 pmid=16211538 | #vanderSpoel2005 pmid=16211538 | ||
Latest revision as of 21:00, 30 June 2008
Gromacs Berendsen1995, Lindahl2001, vanderSpoel2005, Hess2008 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
Tutorials
- Gromacs tutorials
- Free energy calculations with Gromacs (from alchemistry.org)
- See also the share/tutor directory of the Gromacs distribution
References
<biblio>
- Berendsen1995 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.
- Lindahl2001 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.
- vanderSpoel2005 pmid=16211538
- Kutzner2007 pmid=17405124
- Hess2008 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.
</biblio>
