Thank you Professor Case.
Sajeewa
On Wed, Oct 3, 2012 at 7:56 AM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Tue, Oct 02, 2012, Sajeewa Pemasinghe wrote:
> >
> > I am hoping to run production MD with generalized Born solvation scheme
> >
> >
> > I know that N (number of molecules), and T are constant. By default ntp=0
> > so I am allowing the pressure to vary. What about the volume? Can I
> > consider it to be constant or changing? The only ensemble I can think of
> > inluding the resulting trajectory is , in N,V,T . This question might
> sound
> > so naive but I really want to get my basics right.
>
> Generalized Born simulations are run in non-periodic boundary conditions,
> so there is no "volume" of the simulation; (or the effective volume is
> infinite.) There is also no pressure per se. The properties of the
> (implicit) water are probably closer to those of a constant pressure
> solvent than of a constant volume one. (My reasoning: the solute could
> change its shape and its partial molar volume without any penalty. This
> is more like the situation with constant pressure than like constant
> volume.) But if the small differences between ensembles are important to
> you, don't use an implicit solvent model.
>
> ...good luck....dac
>
>
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Received on Wed Oct 03 2012 - 07:00:02 PDT
