[DFTB-Plus-User] Rotational DOF in gas phase MD

[Ben Hourahine]

Hello Manuel,

which thermostat are you using? This sounds like the known artefacts
of the Berendsen thermostat (flying icecube effect).

At the moment, as you've observed, only the translational motion is
removed in the code, but with Berendsen the lowest accessible modes
always end up accumulating kinetic energy. It would be possible to
remove the rotational degrees of freedom as well for non-periodic
calculations, but we haven't done this. If rotation were also removed
then using Berendsen thermostating would instead lead to the low energy
collective bend modes of the molecule heating up.

Would the alternative choice of the Andersen thermostat any use? This
thermostat does not have the same pathology (but has other problems - it
prevents collection of some types of autocorrelation data and suppresses
atomic diffusion, but does correctly sample from the NVT ensemble).

As this molecule has bonds between C and H, I'd suggest testing a
shorter time step is probably a good idea anyway, irrespective of
any thermostatting choices.

Regards

Ben

Manuel Dömer wrote:
> Dear DFTB users,
> 
> I have been running an NVT MD of a peptide in gas phase. Time step = 1
> fs. Visual inspection of the trajectory shows a significant amount of
> kinetic energy is being transfered to the rotation of the molecule. Is
> there a way to avoid this, besides probably decreasing the time step?
> I did not find anything related to this in the manual or an earlier
> post.
> I have set KeepStationary = Yes, but this only affects the
> translation, as I understand.
> 
> Many thanks in advance and best wishes,
> 
> Manuel
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     Dr. B. Hourahine, SUPA, Department of Physics,
   University of Strathclyde, John Anderson Building,
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