From: Sebastian Stolzenberg (s.stolzenberg_at_gmail.com)
Date: Fri Sep 18 2009 - 18:26:42 CDT
Let's assume I have one water molecule within a protein, i.e. it is
known to be only one.
This water may have two different positions within the protein, being
apart by about 4A.
I would like to calculate the free energy between these two different
- Using "pulling" PMF, I expect to face large free energy barriers along
the transition between the two positions. Also, I will have to think
hard about restraints, keeping the protein fixed, etc., so I try to
avoid this PMF option.
- Instead, I would like to use an FEP approach, letting the water
disappear in one position and appear in the other position.
Have you guys experienced any convergence problems in this manner and
how to circumvent them? I hope that the appearing atom will not cause
too many clashes along the transition...
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