From: CHINDEA Vlad (vchindea_at_hotmail.com)
Date: Wed Jan 14 2009 - 17:08:48 CST
I am doing an MD of a protein in a water box with NPT conditions (310 K temperature). In order to check the sanity of the simulation I have done a temperature estimation by fitting Maxwell-Boltzmann distribution to the equilibrated velocity data as explained in the tutorial, but although the temperature reported in the log file looked quite OK (305-313 K) the result obtained by fitting was just 254 K ! What is more strange is that the peak of the kinetic energy distribution is higher then 1 (about 1,2-1,3) which is statistically (and physically) impossible. Since the initial run was just 24 ps I though that maybe I did not equilibrated the system enaugh so I restarted the simulation for another 30 ps, but the result was about the same both in fitted temperature (251 K) and distribution peak. As suggested in http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/1354.html I have corrected also the mathematical expresion of the distribution from (kT)^3 (as shown in the tutorial) to (kT)^3/2.
The step size was 2 fs and RigidBonds was on. Is it possible that this might have such a deleteriouse effect on the fit due to the missing degrees of freedom ?
I understand that I will never get the expected temperature due to the finite size of the system but the difference from 250 to 310 K seems quite large to me. Please let me know if you need anything else in order to see what might be wrong.
Many thanks and kind regards
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