how to visualize an alchemical FEP transformation??

From: Bruno Luís Pinto de Oliveira (
Date: Thu Oct 20 2011 - 06:27:47 CDT

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 ??

Thank you very much for your help


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