From: OMAR NABEEL ALY DEMERDASH (ondemerdash_at_wisc.edu)
Date: Wed Nov 22 2006 - 11:54:21 CST
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.
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