Re: high temperature, 498K, unfolding simulations

From: Michael Grabe (
Date: Thu Nov 13 2003 - 12:31:28 CST

Some thoughts,

You might guess that the average velocities should be about sqrt(2)
bigger at this higher temperature. And the velocity-verlet algo. is
order in time (i think, someone correct me if i am wrong). Then for the
same order accuracy in your velocities you would want your time step
to decrease by dt*2^(-1/4). This isn't too much smaller than dt.
Might be ok. But maybe since the velocity distribution is more spread
at 500K you will run into problems with the higher temperature atoms.

michael grabe

On Thursday, November 13, 2003, at 09:47 AM, james tomomi macdonald

> Dear all,
> I have noticed in a recent paper (PNAS vol 100, p13287) from Daggett's
> and
> Fersht's groups that they have been using a 2fs time step at 498K
> (although they weren't using NAMD). I am wondering if such a long time
> step is a good idea at this temperature and am currently running
> simulations with 1fs time steps and 2fs time steps at 500K to see what
> differences there are.
> I'm curious what other people's opinions are on this.
> Cheers,
> James.
Michael Grabe, Ph.D.
Post-doctoral Fellow
Howard Hughes Medical Institute
University of California, San Francisco
533 Parnassus Ave.
San Francisco, CA 94143
tel: ++ 415.476.6585

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