Andy Shelley 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
You have to take bond length constraints into account (LINCS and Settle)! Best, Jochen > 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 > > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ************************************************ Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ************************************************ _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
