Potential Mean Force Calculation

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Potential Mean Force Calculation

Mark F
Greetings,

I was wonder if there's some way to determine the PMF between to molecules along a specific reaction coordinate of interest using the Geometry-Distance-Restain tool? How can I program Abalone to, for example, automatically perform a 0.1A adjustment to the restraint every so many MD time steps?

Thanks
Mark

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Re: Potential Mean Force Calculation

agilemolecule
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Dear Mark,

Probably you can write your own monitor on Javascript.
Look at the Javascript examples in the .\Scripts folder and on the www page:
http://www.biomolecular-modeling.com/Abalone/manual-Scripts.html

However I did not face with such task. If there are difficulties please let us know. If you manage to do this, we can add your script in the package, if you like.