From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Thu Feb 27 2014 - 07:05:00 CST
For a disappearing solute, just provide the standard, complete topology file (solute + solvent), and define the disappearing atoms in the FEP file.
If you activate the TI version of alchemical transformations (alchType ti), you'll get the derivative you need.
----- Original Message -----
> Dear NAMD users,
> I know that NAMD require a dual topology for initial and final states, in
> order to perform FEP calculation, if all solute atoms disappear(solute turn
> to an ideal gas particle) when moving from lambda 1 to lambda 0 , should the
> solute topology be used as the dual topology?
> I also need derivative of Hamiltonian vs coupling parameter, how can i get
> this from NAMD?
> Javad Noroozi
> Chemical Engineering Department
> Sharif University of Technology
> Email: jnoroozi_at_che.sharif.ir
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