Re: FEP/binding free energy difference WT vs Mut

From: Jerome Henin (heninj_at_gmail.com)
Date: Mon Feb 16 2009 - 11:18:50 CST

Hi Chris,

> 2) since the positive charge of the arginine disappears, I guess I need a
> ion to appear in lambda=1?
> In the purest sense, yes. But this is generally not done and results in
> reasonably dG or dA estimates. Further explanation can be provided if
> needed.

Actually, it would be great if you could provide further explanation,
as this question has surfaced time and again on this list, but has
never, I feel, received a complete and final answer, based on the
specifics of NAMD's PME implementation.

Jerome

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