[gmx-users] Lindemann parameter

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Apr 2 10:08:54 CEST 2010


Hi Dmitri,

Better to start a new thread for a new issue.
It would also help if you give an equation for the Lindemann
parameter. Is it really about fluctuations in the intermolecular
distance, or in the intramolecular distance? The first would be a bit
tough. For the latter you want to have a look at g_rmsdist. It can
produce a matrix of distance fluctuations, which you could
postprocess.

Hope it helps,

Tsjerk

On Fri, Apr 2, 2010 at 9:10 AM, Dmitri Dubov <ddubov at ngs.ru> wrote:
> 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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-- 
Tsjerk A. Wassenaar, Ph.D.

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



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