[gmx-users] a question about ensemble

[Erik Marklund]

4 maj 2012 kl. 10.45 skrev Dommert Florian:

> On Thu, 2012-05-03 at 18:43 +0200, Patrick Fuchs wrote: 
>> Hi Florian,
>> 
>>>> I remark that Langevin method is used also for explicit water system!
>>> 
>>> But there a big question arises to me. The thermostatting by Langevin is
>>> achieved due to random kicks. If I simulate all atoms explicitly, there
>>> is only vacuum between the atoms. Where do the random kicks come from
>>> and how do I set gamma, which is actually related to the viscosity of
>>> the medium I am simulating in? If my medium is vacuum, then gamma should
>>> be zero, shouldn't it, and gamma=0 means no coupling, and hence,
>>> Newton's equation of motion are recovered.
>>> 
>>> I am not an expert with the Langevin thermostat, so this are serious
>>> questions that arise to me now. Furthermore I also thought, that
>>> Langevin dynamics were exactly established for a description of a system
>>> within a medium.
>> The use of Langevin dynamics (SD) to mimic solvant implicitely or as a 
>> thermostat in explicit systems depends on the friction coefficient you 
>> choose. It has to be chosen with care, see for example 
>> http://dx.doi.org/10.1007/b99427 or the GROMACS manual. In explicit 
>> simulations, SD with the appropriate choice of friction coefficient can 
>> be seen as a local thermostat. The advantage is that it samples the 
>> canonical ensemble (in the old versions of GROMACS it was the only way 
>> to get the canonical ensemble before the implementation of Nose-Hoover 
>> or velocity rescaling).
> 
> Hi, thank you very much for pointing to this very interesting article.
> However, though the method seems to work, gamma has a very big
> influence. I also think, that this kind of coupling is not a good
> picture for an explicit simulation, because there is nothing in space
> where friction can arise from, so a reference how to obtain gamma is not
> given. 
> 
> But thanks everybody of you for the nice discussion.
> 
> /Flo

Interesting discussion indeed. I'm just thinking that there might be no fundamental difference to other thermostats. There's nothing in the way that causes the friction, but then again, there's no physical particle that causes the stochastic term in v-rescale, and the Nosé-Hover particle is not physically "touching" the atoms either.  In all cases the surroundings couples to the atoms in a way that can't be seen in e.g. a test tube.

Erik

> 
>> Ciao,
>> 
>> Patrick
>> -- 
>> _______________________________________________________________________
>> Patrick FUCHS
>> Dynamique des Structures et Interactions des Macromolécules Biologiques
>> INTS, INSERM UMR-S665, Université Paris Diderot,
>> 6 rue Alexandre Cabanel, 75015 Paris
>> Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-43-06-50-19
>> E-mail address: patrick.fuchs at univ-paris-diderot.fr
>> Web Site: http://www.dsimb.inserm.fr/~fuchs
> 
> -- 
> Florian Dommert
> Dipl. - Phys.
> 
> Institute for Computational Physics
> University Stuttgart
> 
> Pfaffenwaldring 27
> 70569 Stuttgart
> 
> EMail: dommert at icp.uni-stuttgart.de
> Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
> 
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-----------------------------------------------
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 6688        fax: +46 18 511 755
erikm at xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html

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