A few more questions added to my first response. When calculating the Temperature should I use the mass of the molecule or of the atoms times the velocity of the atoms or velocity of the molecule? Also, when looking at the output of g_traj if I create a small group of atoms close to each other, say 10-12 atoms, the temperature of these atoms varies alot while the temperature the whole system does not, why is this? Is there a way to accurately determine the temperature of a small number of atoms?
Thanks again, Andy On Mon, Sep 22, 2008 at 10:42 AM, Andy Shelley <[EMAIL PROTECTED]>wrote: > 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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