dear amber users,
i'm trying to perform PMF calculations for small charged molecules
approaching to the center of a self assembled monolayer (with heads of
the opposite charge).
beyond of the feasibility of the model, i was wondering if there is
any way of restraining the movement of the ligand just in one
dimension, let's say, apply a soft restraint in x (the umbrella
biasing potential), but also, a much stronger condition to completely
prevent the displacement of the ligand in the other directions.
Otherwise (with just the distance restraint), the molecule tend to
reach the monolayer to interact with the other charged groups.
i should add that i'm not actually interested in studying a real path
of interaction, but instead, i'm looking for energetic differences
between molecules through this particular reaction coordinate (normal
to the SAM).
do you have any suggestions on how to achieve these goals? and, how
will this affect the PMF calculation? is it valid to calculate PMF in
1-D even when more than one restriction is applied?
I thank you in advance for your replies,
regards,
Joan Montes de Oca
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Received on Mon Nov 03 2014 - 17:00:03 PST
