VMD-L Mailing List

From: nettles (jnettle_at_emory.edu)
Date: Mon Jul 19 2004 - 16:01:02 CDT

How did you measure the local temperature?

This is probably a Sybyl specific issue, so you can reply directly.
(off list)

Jim Nettles
Chemistry/Pharmacology
Emory University

On Jul 19, 2004, at 4:45 PM, vlad.chindea_at_pharmatech.ro wrote:

> 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
>