[gmx-users] Calculation of Temperature of Cluster

[Justin Lemkul]

On Mon, Apr 8, 2013 at 9:39 AM, Rasoul Nasiri <nasiri1355 at gmail.com> wrote:

> One suggestion,
>
> Is there any chance to retrieve trajectory of un-evaporated molecules using
> one of gromacs tools? Now I have a ndx file which show number of atoms
> stayed in drop,
>
>
Sure, that's what trjconv does.


> Which one is better? I mean if I can get trajectory (position+velocity)
> unevaporated molecules, I would be able estimate the temperature as well.
> Is it correct?
>
>
I suppose so. You can (in theory) use g_traj or g_clustsize to extract
temperature, and the analyzed atoms can be chosen as an index group of a
larger system or simply that subset that has already been parsed out of the
trajetory. Either approach should be equivalent.

-Justin

-- 

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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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