Orbeckst: /* References */

2008-06-30T21:00:31Z

References

← Older revision		Revision as of 21:00, 30 June 2008
Line 21:		Line 21:
	== 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

Orbeckst: basic Gromacs stuff + refs (uff)

2008-06-30T20:58:53Z

basic Gromacs stuff + refs (uff)

New page

'''[http://www.gromacs.org/ Gromacs]''' <cite>Berendsen1995, Lindahl2001, vanderSpoel2005, Hess2008</cite> is a MD package developed in Groningen, Netherlands, which is published under the [http://www.gnu.org/copyleft/gpl.html GNU Public license]. It's [http://www.gromacs.org/features/index.php 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 [http://pdb.finkproject.org/pdb/search.php?summary=gromacs contained] in the [http://fink.sourceforge.net/ Fink] distribution.

== Documentation ==
Gromacs comes with quite extensive [http://www.gromacs.org/content/view/13/27/ documentation] (accessible through their home page). Especially helpful are
* [http://www.gromacs.org/component/option,com_wrapper/Itemid,192/ Online Reference] manual
* [http://wiki.gromacs.org/ Gromacs Wiki]
* [http://www.gromacs.org/content/view/161/203/ Mailinglist archives]

== Tutorials ==
* [http://www.gromacs.org/content/view/137/182/ Gromacs tutorials]
* [http://www.alchemistry.org/wiki/index.php/Gromacs_Tutorials Free energy calculations] with Gromacs (from [http://www.alchemistry.org alchemistry.org])
* See also the <tt>share/tutor</tt> 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:[http://dx.doi.org/10.1007/s008940100045 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:[http://dx.doi.org/10.1021/ct700301q 10.1021/ct700301q].
</biblio>

[[Category:Gromacs]]
[[Category:Software]]

Gromacs - Revision history

Orbeckst: /* References */

Orbeckst: basic Gromacs stuff + refs (uff)