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

[Ran Friedman, Biochemisches Inst.]

Hi Ben and list readers,

A pretty recent thermostat by Bussi and Parrinello is based on the Berendsen 
thermostat but seems to alleviate the artefacts associated with it:
http://link.aip.org/link/?JCPSA6/126/014101/1

You may want to consider applying it in DFTB.

Ran

On Fri, 19 Feb 2010 12:29:08 +0000
  Ben Hourahine <benjamin.hourahine at strath.ac.uk> wrote:
> 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,
>          107 Rottenrow, Glasgow G4 0NG, UK.
>    +44 141 548 2325, benjamin.hourahine at strath.ac.uk
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> registered in Scotland, with registration number SC015263
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