Dear Amber list,
I have a question concerning QM/MM umbrella sampling. I would like to
simulate ion dissociation in a system made of small organic molecule and
anion in organic solvent. In the system I assume weak interaction between
anion and molecule. I chose axis y as a reaction coordinate for the
dissociation. In the simulation, I use harmonic distance restraint between
the anion and COM of two atoms in molecule. Problem is, that during the
simulation, the anion is moving not only in the y direction but also
perpendicularly to the plane of molecule. Is this behavior correct when I am
interested in the dissociation curve? Or do I need to use another restraint
e.g. for torsion angles? I am not sure, how additional restraints can
influence the computed energy. I also tried fxyz = 0,1,0 but I didn't do
what I wanted.
Thank you for the reply,
Veronika
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Received on Thu Feb 08 2018 - 02:30:03 PST
