[gmx-users] FEP

Mark Abraham Mark.Abraham at anu.edu.au
Thu Mar 23 20:25:56 CET 2006

David Mobley wrote:

> I am rather nervous about doing FEP/TI for disappearing charged 
> molecules, as it is not at all clear to me that it is possible do this 
> correctly with current methods. Perhaps someone else may be able to 
> comment more, but at least with long range electrostatics (PME), systems 
> are required to be neutral. It IS possible to apply PME to a "charged" 
> system, but I think this is typically done by spreading a uniform 
> neutralizing charge throughout the box. It isn't clear that this is 
> really correct for FEP/TI, I don't think, since in that case you will 
> have a charged molecule overlapping with some of the uniform 
> neutralizing charge, which could give strange energy artifacts.

In general, PME can be applied to a system with any charge. The PME 
section of the gromacs manual is silent on this topic, and I've never 
tried to do it, however. You are correct about the uniform neutralizing 
charge throughout the box, but this is present for *every* partial 
charge in the system, each of which contributes individually in the 
Ewald summations. The utility of that as a physical model is a different 
question, however.

I can't comment on the effectiveness of PME on such a system with FEP/TI.


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