I think there may be multiple notions of diffusion being used here.
If you are just talking about the relative position of molecules in a
simulation cell, then I think Aron is correct, there's no difference except
that periodic boundary conditions might cause artifacts.
What Jason described sounds like the diffusion due to dynamics (*i.e.* time
dependence) which can only be calculated from an ensemble of NVE
trajectories (presumably taken with appropriate weights for a given
temperature, pressure, *etc.* distribution. All stochastic thermostats (and
the deterministic Berendsen thermostat) cannot be used to get the time
dependence directly. I've seen it argued that a Hoover-type thermostat is
appropriate (approximately?), but I don't know the exact theory that is
invoked.
Regards,
Brian
On Thu, Nov 8, 2012 at 11:30 AM, Jason Swails <jason.swails.gmail.com>wrote:
> On Thu, Nov 8, 2012 at 4:28 AM, Rajeswari A. <rajeswari.biotech.gmail.com
> >wrote:
>
> > Dear Amber Users,
> > I want to simulate multiple number of proteins in a box. I am very
> confused
> > in choosing what MD method will be useful to solve my problem. Can i do
> it
> > with regular molecular dynamics simulations? I am not sure whether
> > diffusion of solutes are taken care in standard MD. Is there any special
> > method where i can do simulate multiple proteins in a box?
> >
>
> There's no reason you can't simulate a box that contains numerous monomers.
> Note, however, that due to the periodic boundary conditions, your monomer
> concentration is likely to be very high unless you use a very large box.
> This may lead to artifacts, and should be kept in mind.
>
> There is nothing in the theory of molecular dynamics that prevents solute
> diffusion from occurring. In molecular dynamics programs, you typically
> impose PBC and simulate only one solute. As such, the motion of one solute
> is replicated to infinity in all 3 dimensions, which doesn't give you real
> 'diffusion', and can lead to the 'flying icecube' effect (especially with
> the Berendsen thermostat, as I understand it). As a result, COM
> translation of the solute is removed, thereby eliminating solute
> 'diffusion'. If you have multiple monomers, you can get natural diffusion
> even if the COM of all monomers does not translate.
>
> Or you can simply *not* remove the COM (see the "nscm" variable in the
> manual) translation. I can't speak definitively to the wisdom of this
> suggestion, as I've always left nscm as the default value, but as long as
> you don't use a bad thermostat (like Berendsen), the 'flying ice cube'
> effect should not really be an issue (I suggest Langevin dynamics in this
> case).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Thu Nov 08 2012 - 09:00:04 PST
