[gmx-users] how to get averaged coordinates for a residue in a time interval?

[Dmitri Dubov]

Hi all,

One more similar question:

How can I get (in the quickest way!) any form of the Lindemann parameter for rather big molecular crystal? 
(I mean averaged relative fluctuations in the intermolecular distance)

> Well, you could also use g_rmsf with -b and -e, and a suitable index file...

> Cheers,

> Tsjerk

> On Thu, Apr 1, 2010 at 6:18 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:


>> Wu Rongqin wrote:

>>> Dear all,

>>> How to get the averaged coordinates for a short time range say, 10 ps?
>>> which utility should be used?

>> g_traj to extract the coordinates, g_analyze to do averaging.

>> -Justin


>>> r. q.


>> --
>> ========================================

>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> 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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> -- 
> Tsjerk A. Wassenaar, Ph.D.

> post-doctoral researcher
> Molecular Dynamics Group
> Groningen Institute for Biomolecular Research and Biotechnology
> University of Groningen
> The Netherlands

-- 
Regards,
 Dmitri                          mailto:ddubov at ngs.ru
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