[gmx-users] Rised temperatures

[Anton Feenstra]

Christoph Freudenberger wrote:
> Ing. Vojtěch Spiwok wrote:
> 
>> Dear Gromacs users/developers
>> I'm running MD of solvated protein in Berendsen temp.
>> coupling (tau_t = 0.2) and in Parinello-Rahman presure
>> coupling. Bond lenghts are constrained. The temperature
>> of the system is rised (approx 20 K) from ref_t for whole
>> (1 ns) simulation. Is it normal or is it error / incompatibility
>> in settings ? Is it possible to reduce it by increasing of
>> tau_t ?
> 
> 
> Do you use different temperature groups for protein and solvent?
> This is important. Check the manual about it (p. 24).

Cut-off generates heat.

Increasing tau_t helps, but too small may induce oscillations.
You can use Ewald in stead of twin-range for electrostatics,
or use shifted functions (not recommended, there are other
artefacts with that!).


-- 
Groetjes,

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