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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Received on Thu Nov 08 2012 - 09:00:02 PST
