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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