ABF simulations with barriers (adsorption)

From: Zachary Ulissi (zulissi_at_mit.edu)
Date: Mon Jun 10 2013 - 12:26:49 CDT

I'm doing simple adsorption energy calculations using ABF onto a hard
surface (one coordinate). Everything works fine, but often the simulation
gets stuck trying to resolve the potential very near the surface, which is
very large but not interesting or important.

I've tried restraining the colvar to a minimum of several angstroms from
the surface which helps, but the offset is different for each molecule
(different adsorption distances), and if it's too large the minimum in the
resulting PMF is missed.

Does anyone have a good suggestion for doing ABF calculations when there is
a hard wall present?

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