Re: question on free energy pert.

From: Chris Chipot (
Date: Wed Nov 22 2006 - 14:05:58 CST


this can be readily achieved by defining a hybrid topology of your
residue, as outlined in the tutorial available on the NAMD webpage.

In that hybrid topology, both the reference and the target states
coexist. Use PSFgen to generate a PSF that will evidently contain
undesired valence and dihedral angles over atoms common to the
charged and the uncharged side chain. Jerome Henin's Alchemify,
also available on the NAMD webpage, has been designed to correct
the PSF to ensure that the alternate topologies, though coexisting,
never interact. As an alternative, you can define by hand a list of
excluded atoms in your hybrid topology with a patch to remove the
superfluous internal degrees of freedom.

In any case, I do recommend to look at the tutorial, which is rather

Chris Chipot

> Hello,
> I would like to run a free energy perturbation simulation in which the charges of a residue are gradually being turned off. The
> initial state is just the standard residue, but my final state is a residue without charges that has been defined as a new residue
> in my modified topology file (i.e., same atoms, just zeroed-out charges). My question is, how would I set up my psf file for
> this? It is clear how to set up my .fep file, but it isn't clear how to set up a psf.
> Thanks,
> Omar Demerdash


Chris Chipot, Ph.D.
Equipe de dynamique des assemblages membranaires
Unité mixte de recherche CNRS/UHP No 7565
Université Henri Poincaré - Nancy 1 Phone: (33) 3-83-68-40-97
B.P. 239 Fax: (33) 3-83-68-43-87
54506 Vandœuvre-lès-Nancy Cedex, France


       To sin by silence when we should protest makes cowards out of men
                                                     Ella Wheeler Wilcox

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:42:51 CST