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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Received on Tue Feb 12 2013 - 13:00:02 PST
