[gmx-users] g_msd, REMD, trestart...

Julián GC jgelcon at yahoo.com.ar
Fri Mar 14 18:20:29 CET 2008

		@page { size: 8.5in 11in; margin: 0.79in }
		P { margin-bottom: 0.08in }

I'm studying small water clusters with Gromacs 3.3 (I'malso performing MC with a self-writed MC program).
I run 24 boxesin paralell, with -replex 100000 (it is important to use replicaexchange).

I need to get MSD results, but I don't think g_msdtakes into account that every 100ps the boxes are beingexchanged.

Does anyone knows how to fix that? Have anyone hadto deal with something like this before?
(The obvious "easy"solution is to chop the trajectory in blocks of 100ps, calculate MSDin each block, and then average all the results, but would be nice ifthis annoying "shortcut" could be avoided)

Thank youvery much in advance,

Julian Gelman Constantin 
Departmentof Inorganic, Analytic and Chemical Physics (DQIAQF) 
School ofExact and Natural Sciences 
University of Buenos Aires, Argentina

      Yahoo! Encuentros.

Ahora encontrar pareja es mucho más fácil, probá el nuevo Yahoo! Encuentros http://yahoo.cupidovirtual.com/servlet/NewRegistration
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080314/ff2105a8/attachment.html>

More information about the gromacs.org_gmx-users mailing list