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

Mon Feb 22 10:30:58 CET 2010

PS There is potentially better thermostat available now, by Leimkuhler (J Stat Phys 135 (2009) 261-277) - it appears to be more rigorous in proving its ergodicity, for example.

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From: dftb-plus-user-bounces at dftb-plus.info [mailto:dftb-plus-user-bounces at dftb-plus.info] On Behalf Of Manuel Dömer
Sent: 22 February 2010 09:28
To: dftb-plus-user at dftb-plus.info
Subject: Re: [DFTB-Plus-User] Rotational DOF in gas phase MD

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.

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Message: 1
Date: Fri, 19 Feb 2010 12:29:08 +0000
From: Ben Hourahine <benjamin.hourahine at strath.ac.uk<mailto: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<mailto:dftb-plus-user at dftb-plus.info>>
Message-ID: <4B7E8414.8090601 at strath.ac.uk<mailto: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
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Message: 2
Date: Fri, 19 Feb 2010 13:37:33 +0100
From: "Ran Friedman, Biochemisches Inst." <r.friedman at bioc.uzh.ch<mailto:r.friedman at bioc.uzh.ch>>
Subject: Re: [DFTB-Plus-User] Rotational DOF in gas phase MD
To: benjamin.hourahine at strath.ac.uk<mailto:benjamin.hourahine at strath.ac.uk>, User list for DFTB+ related
          questions <dftb-plus-user at dftb-plus.info<mailto:dftb-plus-user at dftb-plus.info>>
Message-ID: <web-22135993 at idmailbe1b.unizh.ch<mailto: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: