Re: how to do free energy perturbation calculation in NAMD?

From: Jérôme Hénin (
Date: Mon Feb 13 2006 - 07:23:50 CST

Le Mardi 7 Février 2006 18:21, a écrit :
> Dear all,
> I am following the tutorial for setting up alchemical free energy
> perturbation calculation in NAMD. However, it's still not clear to me how
> to actually run the calculation.
First, I have to admit that the tutorial needs to be updated, which I am going
to do very soon - hopefully. The main point I have to mention is that you can
do everything using psfgen, and that you should also use a tool called
alchemify (see

> Here are my questions.
> First, how should I define the dual-topology if the residues (RESI)
> involved are identical before & after the alchemical transformation, but
> the patch residues (PRES) are different?
It is hard to tell without knowing the details of your transformation, but I
guess the best way would be to modify the patch itself, to include both

> Second, what is the complete NAMD script for the free energy perturbation
> calculation? I think in the turtorial, it only shows the "FEP" part.
The rest of the NAMD script is what you would use to run a traditional MD
simulation, and it is system-dependent. It is up to you to decide the
simulation conditions you want to use.

If you are not yet familiar enough with MD and NAMD to write such a script, I
urge you to learn more about that before you try running FEP simulations.


Jérôme Hénin
Equipe de Dynamique des Assemblages Membranaires
Université Henri Poincaré / CNRS
Tel : (33) 3 83 68 43 91        Fax : (33) 3 83 68 43 87

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