Re: FEP/binding free energy difference WT vs Mut

From: Luis Cunha (
Date: Tue Feb 17 2009 - 11:50:20 CST

Dear Chris and Jerome,
thank you very much for your answers. They are very helpful. I'll try
to set up these two FEP simulations and hope it goes smoothly.

Chris, I don't want to bother too much, but if you could explain
further why it's not required that the charge disappears in lambda=1,
it would be great for users like me that are not experts in this

Thank you,

>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.

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