Hi,
> I agree with your comment. I think what puzzles me is the scmask
> keyword. For example if I use scmask='x,y' for state 0 and scmask='x'
> for state 1, or use scmask='y' for state 0 and scmask=' ' for state 1,
> assuming everything else is the same, am I going to get the same dv/dl
> for each transformation step?
correct, with sufficient sampling that should be true. But in all normal
cases, including the one we discuss here, everything else will *not* be
the same, since the transformation including x in the scmasks will start
from a molecule with different atomic partial charges than the
transformation in which x is a common atom (namely differing in the charge
on x), leading to a different conformational ensemble.
Kind Regards,
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Fri May 06 2011 - 01:30:04 PDT
