Thank you very much Aron, Jason and Brian for your valuable suggestions.
On Thu, Nov 8, 2012 at 10:20 PM, Brian Radak <radak004.umn.edu> wrote:
> 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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> > AMBER.ambermd.org
> > 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
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Received on Thu Nov 08 2012 - 23:30:02 PST
