[gmx-users] Vacuum simulation freezes the system

Bert de Groot bgroot at gwdg.de
Wed Oct 13 16:17:33 CEST 2004

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 ;-)



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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