[gmx-users] Vacuum simulation freezes the system

[Anton Feenstra]

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?

-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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