[gmx-users] Calculating Temperature from Velocity

[Jochen Hub]

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 at 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 gmx-users-request at gromacs.org.
> 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
************************************************