Re: Free-energy perturbation in NAMD: Evaluation of electrostatic and van der Waals terms

From: felmerino_at_uchile.cl
Date: Tue Nov 09 2010 - 00:38:58 CST

Hey,

Probably, it is not a good idea to suppose that every person on the list have the book that you are citing (yet they should, the are some very good
explanations in there). Anyways, the implementation of the soft core potentials for the alchemical calculations are here http://www.ks.uiuc.edu/Research/namd/2.7/ug/node52.html. If i am understanding well what are asking, the files that you need is ComputeNonBondedFEP.C and ComputeNonBondedBase.C (but it was just a fast look).

best

Felipe

----Mensaje original----
De: christian.jorgensen_at_merton.ox.ac.uk
Fecha: 08-11-2010 19:23
Para: "namd-l_at_ks.uiuc.edu"<namd-l_at_ks.uiuc.edu>
Asunto: namd-l: Free-energy perturbation in NAMD: Evaluation of electrostatic and van der Waals terms

Hi all,
In the book Chipot and Pohorille "Free Energy Calculations", Springer, there is an equation (2.49) for the modification of the parametrization of the van der Waals term in the potential energy function that governs the interaction of an appearing or disappearing atom i with an unaltered one j.

My question: How is this equation coded in the src directory of NAMD?

I am only just starting my graduate studies and cannot read C / C++ so I do not entirely understand the files in the NAMD src

FreeEnergyGroup.C
FreeEnergyGroup.h
FreeEnergyLambda.C
FreeEnergyLambda.h
FreeEnergyLambdMgr.C
FreeEnergyLambdMgr.h
FreeEnergyMain.C
FreeEnergyParse.C
FreeEnergyParse.h

etc.

My question: I also want to know how NAMD codes the equivalent equation to (2.49) for the electrostatic potential?

Any input here would be much appreciated!
Christian

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:23:22 CST