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Hiall,
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
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