[gmx-users] g_msd clarification

[Dmitry Lupyan]

I'm not sure this information is in my trajectory, the axis in the
msd.xvg only goes up to 600ps (and not 60ns).  Is there anyway i can
set the interval in the trr file?

-dima

On Tue, Apr 14, 2009 at 6:05 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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.
>
> -Justin
>
>> -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
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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