Thank you very much, Aron.
Sajeewa Dewage
On Tue, Feb 12, 2013 at 4:16 PM, Aron Broom <broomsday.gmail.com> wrote:
> the harmonic restraint is between A and B, they move relative to one
> another, and the force is applied equally to both (Newton's laws and all
> that). Absolute coordinates are meaningless in this context.
>
> On Tue, Feb 12, 2013 at 3:51 PM, Sajeewa Pemasinghe <sajeewasp.gmail.com
> >wrote:
>
> > Hi all,
> >
> > In umbrella sampling, I have choosen the distance between the atoms A
> and
> > B as the coordinate and apply the harmonic restraint on the atom B.
> During
> > the simulation atom A can move with respect to the initial position from
> > where I started the simulation. Doesn't this have an effect on the
> accuracy
> > of the PMF calculation? (specially if the relative movement is
> > considerable). But in order to minimize that relative movement if i apply
> > another harmonic restraint on A as well, I would be disrupting the very
> > concept of umbrella sampling on atom B isn't it? In an instance where
> atom
> > A shows considerable relative movement what steps should be taken to
> > preserve the accuracy of PMF data of umbrella sampling on B?
> >
> > Thank you
> >
> > Sajeewa Dewage
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> >
>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
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Received on Tue Feb 12 2013 - 15:00:02 PST
