From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Sun Sep 27 2009 - 16:27:52 CDT
Hi Sebastian,
That should work. You will probably have to apply some kind of
restraint to keep each water molecule in its assigned pocket
(especially the molecule whose interactions are turned off).
Jerome
2009/9/19 Sebastian Stolzenberg <s.stolzenberg_at_gmail.com>:
> Dear All,
>
> 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
> positions.
> - 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...
>
> Thanks,
> Sebastian
>
>
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