[gmx-users] Calculation of Temperature of Cluster

Justin Lemkul jalemkul at vt.edu
Mon Apr 8 15:41:21 CEST 2013

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)


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