[gmx-users] g_msd clarification

Justin A. Lemkul jalemkul at vt.edu
Wed Apr 15 00:05:04 CEST 2009

Dmitry Lupyan wrote:
> Hello Gromacs Users,
> I have a 60ns trr trajectory file (converted with VMD from namd2
> trajectory) which has 6000 snapshots saved at 10 ps intervals.  how do
> I specify the snapshot interval to g_msd so it calculates the D
> properly?

Which option are you referring to?  The only one I can think of is -trestart, 
which has nothing to do with frame interval, but is related to statistics.  You 
shouldn't have to tell any of the Gromacs tools what the frame interval is; if 
you have a valid trajectory, that information is already present.


> -dima
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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