<div dir="ltr">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?<br>
<br>Thanks again,<br>Andy<br><br><div class="gmail_quote">On Mon, Sep 22, 2008 at 10:42 AM, Andy Shelley <span dir="ltr"><<a href="mailto:robert.shelley@gmail.com">robert.shelley@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div dir="ltr">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.<br>
Statistics over 10001 steps [ 995.0001 thru 1000.0001 ps ], 1 data sets<br><br>Energy Average RMSD Fluct. Drift Tot-Drift<br>-------------------------------------------------------------------------------<br>
T-System 299.981 1.36143 1.35806 0.0663083 0.331574<br>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?<br>
<br>Thanks,<br>Andy<br><br><br></div>
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