RE: how to visualize an alchemical FEP transformation??

From: Bruno Luís Pinto de Oliveira (
Date: Thu Oct 20 2011 - 13:28:13 CDT

Dear axel,

Thank you for your reply. I agree with you. I confess that I still have some difficulties in understanding what is behind FEP.

But that´s why I'm studying the FEP principles and trying to understand my results

All of my group work with TI / Amber and nobody can help me.

Moreover, in my opinion the NAMD manual is not that well documented in terms of FEP simulations (the only exception is the good tutorial of Chipot et al.)

The only possibility I have is asking for "your" help in the forum...

My doubt is if the Re(CO)3 core disappear during the FEP simulation the "arms" that are coordenated to it will be free/flexible to interact with the protein??? Or when the Re(CO)3 core is vanished what happens is that only the non-bonded terms are switched off?

I know it is a basic question but I can not find an answer...

Thank you


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