[gmx-users] Calculation of Temperature of Cluster

[Rasoul Nasiri]

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,

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?

Rasoul


On Mon, Apr 8, 2013 at 2:30 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> On Mon, Apr 8, 2013 at 9:24 AM, Rasoul Nasiri <nasiri1355 at gmail.com>
> wrote:
>
> > Justin,
> > Thanks for your comment.
> >
> > Instead of .xtc, I just used .trr in which nstvout isn’t zero. I'm still
> > encountering to empty file for temperature.
> >
> >
> Can you please provide the gmxcheck output for the .trr file? I suppose
> there could be a bug, but we need to rule out a few things first. If
> g_clustsize still fails, you can get the output temperature from g_traj
> -ot, which appears to have a redundant function.
>
> -Justin
>
> --
>
> ========================================
>
> 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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