[gmx-users] temperature

Mark Abraham Mark.Abraham at anu.edu.au
Tue Mar 27 03:00:03 CEST 2012

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.

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