Re: how to visualize an alchemical FEP transformation??

From: Axel Kohlmeyer (
Date: Thu Oct 20 2011 - 14:02:59 CDT

2011/10/20 Bruno Luís Pinto de Oliveira <>:
> 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.

i find it hard to believe that nobody has ever looked at FEP.

> 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 documentation for most simulation packages typically
tells you how a specific set of options can be activated.
the user is expected to learn the theoretical background
from textbooks and original literature.

if that kind of information would be included in
the documentation of a simulation software,
there would be no time left to program the software.

> 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?

why do you believe that this *has* to happen?
have you run a simulation of the final state by itself?
that way you can easily tell whether your initial
assumption is right or wrong. at least this is what
common sense tells me.

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

i would recommend that instead of looking for
"canned" answer to your specific question, you
try to look for some alternate option to validate
your results. whether some random person on
the net gives you his blessing for your results,
has very little value in terms of scientific value
of your work and matching some experimental
results can have many reasons, among them
are sheer luck, error compensation and correct
execution or a combination of them.


> Thank you
> Regards

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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