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

[Manuel Dömer]

Dear Ben,

thank you very much for you explanations and hints. I have been using  
the Berendsen thermostat for reasons associated with other simulations  
on this specific project.
But I definitely will give the Andersen a try. Right now it is  
especially important for me to thermalize the system in a good way.  
For data collection in the production phase, I think I can run NVE  
dynamics.

Many thanks again for your clarifications!

Best Regards,

Manuel

Dear Ran,

thanks for pointing me to the Bussi thermostat.


>
>
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 19 Feb 2010 12:29:08 +0000
> From: Ben Hourahine <benjamin.hourahine at strath.ac.uk>
> Subject: Re: [DFTB-Plus-User] Rotational DOF in gas phase MD
> To: User list for DFTB+ related questions
> 	<dftb-plus-user at dftb-plus.info>
> Message-ID: <4B7E8414.8090601 at strath.ac.uk>
> Content-Type: text/plain; charset=ISO-8859-1
>
> 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 D?mer 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
>> _______________________________________________
>> DFTB-Plus-User mailing list
>> DFTB-Plus-User at dftb-plus.info
>> http://www.dftb-plus.info/mailman/listinfo/dftb-plus-user
>
> -- 
>     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
>   The University of Strathclyde is a charitable body,
> registered in Scotland, with registration number SC015263
>
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 19 Feb 2010 13:37:33 +0100
> From: "Ran Friedman, Biochemisches Inst." <r.friedman at bioc.uzh.ch>
> Subject: Re: [DFTB-Plus-User] Rotational DOF in gas phase MD
> To: benjamin.hourahine at strath.ac.uk, User list for DFTB+ related
> 	questions <dftb-plus-user at dftb-plus.info>
> Message-ID: <web-22135993 at idmailbe1b.unizh.ch>
> Content-Type: text/plain;charset=iso-8859-1;format="flowed"
>
> 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 D?mer 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
>>> _______________________________________________
>>> DFTB-Plus-User mailing list
>>> DFTB-Plus-User at dftb-plus.info
>>> http://www.dftb-plus.info/mailman/listinfo/dftb-plus-user
>>
>> -- 
>>    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
>>  The University of Strathclyde is a charitable body,
>> registered in Scotland, with registration number SC015263
>>
>> _______________________________________________
>> DFTB-Plus-User mailing list
>> DFTB-Plus-User at dftb-plus.info
>> http://www.dftb-plus.info/mailman/listinfo/dftb-plus-user
>
>
>
>
>
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> End of DFTB-Plus-User Digest, Vol 26, Issue 4
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