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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