Re: how to visualize an alchemical FEP transformation??

From: Axel Kohlmeyer (
Date: Thu Oct 20 2011 - 09:02:34 CDT

2011/10/20 Bruno Luís Pinto de Oliveira <>:
> Dear all,
> Recently I published a post in the VMD mailling list asking how to visualize
> an alchemical transformation but I think that the same question is relevant
> to post here.
> I´m doing a FEP transformation which thermodynamic cycle I published in my
> webpage to be easy to understand.
> As you can see in my transformation I did the set up such that the Re(CO)3
> core vanished.
> I was guessing that during the simulation the amines that are coordentated
> to the Rhenium will turn flexible and interact with the protein. What I see
> during the simulation (I loaded the .psf and the .dcd written during the
> simulation) is that the amines are still  coordenated to the Rhenium and the
> rhenium core did not disappear.
> Now I doubt if I did correctly the set up or if the set up is OK and the
> Re(CO)3 is presented during the simulation but in fact is not interacting
> with the protein ???
> Lucky (or not) the caculated results are in good agreement with the
> experimental ones.
> I found this information in the NAMD "manual":
> "It is also worth noting that the free energy calculation does not alter
> intramolecular potentials, stretch,
> valence angle deformation and torsions, in the course of the simulation..."
> That´s why I didn´t see the arms that are coordenated to the metal turning
> flexible?
> Can anyone help me with some comments ??

have you looked at the theory behind FEP?
and particularly have you thought about what
happens in the implementation of it?

your question seems to indicate that you
take the "descriptive explanation" too literal
and are not thinking in the terms of what
the program actually does in order to achieve
the effect that you are discussing (and
confused about).

it is very difficult to discuss your results otherwise.


> Thank you very much for your help
> Bruno

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

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