[gmx-users] Re: Simulation in the high temperature conditions

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Apr 11 11:35:48 CEST 2012

Hey :)

I'd say a protein should be loosing structure at 700K. Can't even say
the force field is wrong there, even though it hasn't been
parameterized for such temperatures for certain. You'd have to check
with experiments.
Trying to do high-temperature simulations is fine. But trying to do
high temperature simulations to get results that match a room/body
temperature ensemble is completely bogus. If you aim to use this
approach for enhanced sampling, you're in for some serious
reparameterization. Part of the deal may indeed be adding
long(er)-range distance restraints. However, the force constants to
use will increase with temperature, and with very high temperatures
the force constants may end up so high that they give rise to fast
oscillations, which will require using a smaller time step.

Just my 2 cents...


Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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