[gmx-users] Vacuum simulation freezes the system
feenstra at few.vu.nl
Tue Oct 19 18:03:02 CEST 2004
Bert de Groot wrote:
> Martin Ulmschneider wrote:
>> 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).
IIRC, there used to be a warning about this by grompp. Is that still
there, or does the check sometimes fail to catch the problem?
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
| | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/ |
| | "If You See Me Getting High, Knock Me Down" (RHCP) |
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