[gmx-users] Vacuum simulation freezes the system
spoel at xray.bmc.uu.se
Wed Oct 13 19:27:06 CEST 2004
On Wed, 2004-10-13 at 16:17, Bert de Groot wrote:
> Martin Ulmschneider wrote:
> > Hi,
> > I have found that during a vacuum simulation my peptide (gly-gly-gly)
> > slowly freezes when i use the Berendsen thermostat. I have checked that
> > this applies to all proteins in vacuum, for example with the nmr1
> > tutorial supplied with the gromacs distribution (just change the number
> > of steps to 100000 or so).
> sounds like the "flying icecube" problem. Be sure to remove overall translation and
> rotation every step (ie comm_mode = angular and nstcomm = 1 in your mdp file).
> > My question is this: How can i perform a realistic simulation in vaccuum
> > that does not freeze? I.e. what do i need to change in the mdp-file?
> "reaslistic" and "vacuum" are two words that don't combine very well when talking
> about protein dynamics ;-)
Unless you are talking about protein dynamics in vacuum! Interesting
e.g. in context of mass spec. experiments.
> Dr. Bert de Groot
> Max Planck Institute for Biophysical Chemistry
> Computational biomolecular dynamics group
> Am Fassberg 11
> 37077 Goettingen, Germany
> tel: +49-551-2012308, fax: +49-551-2012302
> email: bgroot at gwdg.de
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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