VMD-L Mailing List

From: vlad.chindea_at_pharmatech.ro
Date: Mon Jul 19 2004 - 15:45:48 CDT

Dear VMD users

Although I do not use this program for the moment I have run into a
molecular dynamics problem upon which I need your expert advice. I
performed a series of molecular dynamics simulations with Sybyl 6.91 in
NTV ensamble. I was simulating a small molecule inside a box with 1600
molecules of water, after 20 picosecond of simulation the temperature of
the system was reported as 300K as intended but when I measured the local
temperature of the whole solvent system, the average was around 200K.
Because the solvent accounted for more than 99% of the mass of the system,
I expected a value of solvent temperature of nearly 300K. Another 10ps of
simulation did not change the situation. Thermostat coupling constant was
20 femtoseconds, and implicit thermostat in Sybyl is, I think, Berendsen.

Could you be so kind and inform me: is there a bug in temperature
calculation or my expectations were wrong considering the situation ?

Looking forward to your answer
Many thanks and best regards
Vlad chindea

Phd student , Romania