[gmx-users] Vacuum simulation freezes the system

Lars Schaefer Lars.Schaefer at mpi-bpc.mpg.de
Wed Oct 13 16:32:32 CEST 2004

Hi Martin,

do you apply center of mass motion removal?
(i.e., for gas phase simulations, mdp-option "comm-mode = angular")

Otherwise, all the internal energy might be transformed into translation 
/ rotation of the overall system.

Cheers, Lars

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).
> 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?
> Best wishes,
> Martin
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Lars Schäfer
MPI for biophysical Chemistry
Theoretical and computational Biophysics group
Department 070
Am Fassberg 11, D-37077 Goettingen
Tel: 0049 551 201-2305, Fax: 0049 551 201-2302
E-Mail: Lars.Schaefer at mpi-bpc.mpg.de
Home: http://wwwuser.gwdg.de/~lschaef2/homepage.html

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