[gmx-users] g_msd clarification

[Justin A. Lemkul]

Dmitry Lupyan wrote:
> 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?
> 

Use gmxcheck to check the contents of the .trr file, which will include frame 
interval.  If it is wrong (i.e., a consequence of the conversion from NAMD -> 
GMX), use trjconv -timestep.

-Justin

> -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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> 

-- 
========================================

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

========================================