From: Hannes Loeffler (Hannes.Loeffler_at_stfc.ac.uk)
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
-- Scanned by iCritical.
This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:22:28 CST