Subject: MD/NVE. E/T fluctuations. What's too much?

From: "Gustavo A. Mercier Jr" <[email-masked]>
Date: Tue, 29 Oct 1996 12:33:18 -0500 (EST)

Hi, CCLer's

I am running some MD simulations (a biorganic solute in H2O) using
amber and need some guidance.

What is too much of an energy fluctuation when running an NVE
ensemble? The temperature is not fixed but targeted to 300K. How
much leeway is reasonable in the fluctuations of the temperature
and deviations between the mean temperature and the target temperature?

In running simple Leonnard-Jones potentials, people take 1 in 10^4 as
a reasonable fluctuation in the energy. The amber potential is more
complex. Is 1 in 10^2 reasonable?

Obviously the answer may depend on what I intend to do with the
simulation. I am interested in the frequency spectrum of the
atomic motions of the solute and some radial distribution functions. The
goal is to generate friction coefficients and potentials of mean force
for the atoms in the solute.

Thanks for your kind reply. I will summarize to the net if 
there is enough interest.

Gus Mercier, Jr.
Univ. of Pennsylvania
[email-masked]