[gmx-users] molecular dynamics problems

Xavier Periole x.periole at chem.rug.nl
Tue Jul 20 12:05:51 CEST 2004

vlad.chindea at pharmatech.ro wrote:

>Dear GROMACS 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. 
Why NVT ?? I guess you checked the density of your system ! If you actually
need to run in NVT perhaps an NVE simulation would be nice to equilibrate
the volume first.

>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.
What do you mean by the "local temperature of the solvent system" ? 20 
ps may be
too short equilibration ! Did you assign velocities at the start of the 
simulation ?

>Because the solvent accounted for more than 99% of the mass of the system,
>I expected a value of solvent temperature of nearly 300K. 
You mean 200K ? If the program gives you 300 K for the whole system that 
that the solvent is probably at 300K. Perhaps check your calculation of 
the solvent alone.

>Another 10ps of
>simulation did not change the situation. Thermostat coupling constant was
>20 femtoseconds, and implicit thermostat in Sybyl is, I think, Berendsen.
20 fs constant coupling to the thermostat is way to small !! May be 
better to try 0.1 ps

>Could you be so kind and inform me: is there a bug in temperature
>calculation or my expectations were wrong considering the situation ?
This is unlikely, I guess the programm has been used many time and the
algorithm to get the temperature is not that fancy to make mistakes on it.



   Xavier Periole - Ph.D.

   Dept. of Biophysical Chemistry / MD Group 
   Univ. of Groningen
   Nijenborgh 4
   9747 AG Groningen
   The Netherlands

   Tel: +31-503634329
   Fax: +31-503634800
   email: x.periole at chem.rug.nl
   web-page: http://md.chem.rug.nl/~periole

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