Re: high temperature, 498K, unfolding simulations

From: Brian Bennion (
Date: Thu Nov 13 2003 - 12:23:13 CST

Hello James,

I graduated from the Daggett group this spring, so I can give you and
others some insight.

First, there is a recent JMB paper that describes the rationale for high
temp simulations and its effects on the PE landscape

Increasing temperature accelerates protein unfolding without changing the
pathway of unfolding
Day R, Bennion BJ, Ham S, Daggett V
322 (1): 189-203 SEP 6 2002
The long step, which I considered very short until 4 months ago, can be
used because of the integration scheme ENCAD (the md engine used) is very
efficient and accurate in conserving energy (modified beeman algorithm)
under very short cutoffs (~6-8A).

The verlet code in namd chokes at 2fs on large systems, if the same
cutoffs are used as described in the Daggett group literature. It even
chokes on large systems with long cutoffs of 10A.

If you can get something running for more than 1ns in namd with a 2fs
timestep at 500K I would be impressed.
Its not NAMDs fault that this occures, just the integration scheme.

I have brought this up with Jim Phillips in the past and have poked around
in the code to see how I could implement the modified beeman in NAMD as an

Anyway, I can take more questions if you want. I don't know if there are
other Daggett group members on the list yet.


 On Thu, 13 Nov 2003,
james tomomi macdonald wrote:

> 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.

**Brian Bennion, Ph.D.                                         **
**Computational and Systems Biology Division                   **
**Biology and Biotechnology Research Program                   **
**Lawrence Livermore National Laboratory                       **
**P.O. Box 808, L-448                     **
**7000 East Avenue       phone: (925) 422-5722                 **
**Livermore, CA  94550   fax:   (925) 422-6605                 **

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