[gmx-users] Calculating Temperature from Velocity

[Andy Shelley]

I am trying to calculate the temperature from the final velocity posted in
the confout.gro file after a simulation runs. I have implemented a berendsen
thermostat to control the temperature to 300K and ran it for 1ns. Looking at
g_energy the final temperature of the system is 299.981.
Statistics over 10001 steps [ 995.0001 thru 1000.0001 ps ], 1 data sets

Energy                      Average       RMSD     Fluct.      Drift
Tot-Drift
-------------------------------------------------------------------------------
T-System                    299.981    1.36143    1.35806  0.0663083
0.331574
>From the manual section 3.4.3 the temperature can be calculated from T=
sum[mass_i v_i^2] / (#degrees of freedom * boltzmann constant) where number
of degrees of freedom=3N-N_c-N_com. I used N_com =3 because the center of
mass velocities are constants of the motion. If I only control the
temperature does this effect the number of constrants on the system? When I
calculate the temperature by hand with # degrees of freedom =3N-3 I get a
temperature of 317.5. Any ideas why I can not calculate the same temperature
g_energy does?

Thanks,
Andy
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