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 - 13:30:03 PST
