alchemical free energy simulations with parmtop

From: Hannes Loeffler (
Date: Tue Jun 17 2014 - 04:35:59 CDT


I am just looking through a few tutorials on how to do alchemical
relative free energy calculations and see that they are all based on the
PSF topology file format. I wonder if this is a requirement with namd
or a AMBER parmtop file could be used instead.

>From what I understand there could be problems with the force fields
terms in the parmtop because the way it works in namd is to create the
morph pair as a single residue (and describe vanishing/appearing atoms
in an associated PDB file). But is it possible with a parmtop provided
the parmtop is created/manipulated accordingly? I guess this all boils
down to how namd generates the force field terms internally for the two
mutated molecules/fragments.

Many thanks,

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