On Thu, Feb 08, 2018, Veronika Jurásková wrote:
>
> 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?
Yes: this is the "correct" behavior, at least if "correct" means corresponding
to the underlying physical behavior. In reality, the ion and molecule can
interact in many geometries, not just along a single line.
....good luck....dac
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Received on Mon Feb 12 2018 - 05:00:02 PST
