AMBER Archive (2003)

Subject: T in MD vs. T in wet experiments

From: Jianhui Wu (wujih_at_BRI.NRC.CA)
Date: Tue Jun 24 2003 - 20:34:31 CDT

Dear Amber users,

Some time ago, someone asked in the amber group about the difference
between the time in simulation and the time in real world. Now I have a
similar question about temperature.

(1) In the amber MD simulation, we set T =
300 K and try to use the simulation results to explain the wet
experimental results obtained at (said) T2=300K. Now, how sure we can say
that T=T2?

(2) At least some parameters of the forcefield are derived by fitting to
the wet experimetnal data (from room temperature). Is there a best
performance temperature range (in MD) for the forcefield? At elevated
temperature, maybe the forcefield might break down to some extent?

Thanks a lot for your help,

Jian Hui
Lady Davis Institute
McGill University