Hi,
> For states V0 and V1 unperturbed atoms (in other words, the same atoms
> with the same coordinates), do they need to have exactly the same charges?
no, they can but don't have to. This means implicitly that if they do not
have the same charge, your transformation free energy accounts for
changing this charge, plus whatever else is changing in the unique atoms.
The common atom electrostatics is scaled linearly, but that is normally
not a reason for concern.
So you need to make sure to compute free energy changes in which the
overall charge changes cancel out, since they do not contribute meaningful
total energy terms.
Doing the same transformation (e.g. between two ligands with differing
charges) in two environments (e.g. in two different solvents) yields
cancelling internal electrostatics terms and meaningful delta-delta-Gs
So typically, having different charges on common atoms is something that
will occur in your simulations, that will influence dVdl and that is fine
:-)
Thomas
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Received on Mon Dec 10 2012 - 11:30:03 PST
