[gmx-users] Temperature Histogram
jalemkul at vt.edu
Wed Nov 14 13:18:14 CET 2012
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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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