[gmx-users] Temperature Histogram

[Samadashvili Nino]

Thank you for your answer. However, when I use g_energy on .edr file it prints the average temperature of the system and not of the  group of atoms that I am interested in, which is why I was trying to make g_traj work cos it uses index.ndx file for choosing the segment from your system and calculate the average temperature for that segment.
One more thing, g_energy has Pres-XX, XY etc., what are these?

Cheers,

Nino 


________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Justin Lemkul [jalemkul at vt.edu]
Sent: Wednesday, November 14, 2012 2:18 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Temperature Histogram

On 11/14/12 7:10 AM, Samadashvili Nino wrote:
> Dear Justin,
>
>   I have been looking for some option to calculate the average temperature, locally in my system. I found g_traj which I can use with index file and calculate temperature for a particular group in my system but somehow it gives a wrong value (The average temperature (NVT simulation) is 240 K and g_traj outputs 120 K).
> Is there any other option available in Gromacs?
>

g_traj doesn't account for constraints, but the result can be calculated from
what g_traj produces.  That's more complicated than you need, and will not be
accurate over all MD steps.  All you need to do is extract the temperatures from
the .edr file using g_energy and the average is printed to the screen.  This
average is correct over all steps, since energy history is stored in the .edr
file and is not limited to nst* output.

-Justin

--
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
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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