On 27/03/2012 8:23 AM, Roy Roshko wrote:
Dear gromacs users,
Aside from a scale factor, should the time dependence of the
temperature T(t) extracted from the .trr file with g_traj for a given
residue be
Using what command line? Have you read g_traj -h about -ot?
identical to the time dependence of the total kinetic energy
(translational + rotational) K(t) extracted from the .trr file with
g_traj for the same residue? If not, why not? Based on the formal
relationship between the kinetic energy and temperature (T ~ v^2) we
expect them to be identical but our simulations do not yield this
result. Any information would be much appreciated.
There are many things that affect the fine details here, including
GROMACS version, your integrator, thermostat and the frequency of energy
computation and output vs velocity output. So with the available
information there's nothing to say. Do check out chapter 3 of the manual
for discussion of details here.
Mark
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