[gmx-developers] editing the code of the VDW and electric potentials and forces

Shirts, Michael (mrs5pt) mrs5pt at eservices.virginia.edu
Fri Aug 30 14:39:06 CEST 2013

Note that this looks fairly similar to:


The relevant code would be in:

But anton is right in that your proposed code change will mess up energy
conservation, even if the cutoff us 7 kcal/mol -- individual interactions
will go up there fairly frequently, leading to problems in energy

Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu

> From: Asaf Farhi <asaf.farhi at weizmann.ac.il>
> Reply-To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
> Date: Fri, 30 Aug 2013 06:48:48 +0000
> To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
> Subject: [gmx-developers] editing the code of the VDW and electric potentials
> and forces
> Dear GROMACS Developers
> My name is Asaf.
> I'm trying to implement a novel free energy calculation method and interested
> to do a very minor code change.
> I will really appreciate help on this issue.
> What I'm trying to implement in GROMACS is very simple. It's actually only one
> if statement that is relevant to the VDW and Electric energies and forces.
> What is needed is to add for every calculation of energy and force:
> If (E_VDW>Ec)
> {
> E_VDW=Ec;
> f_VDW=0;
> }
> If (E_EL>Ec)
> {
> E_el=Ec;
> f_el=0;
> }
> where E_VDW is the energy associated with the pair VDW interaction, f_VDW is
> the force associated with the pair VDW potential and Ec is a constant.
> In addition I need to multiply specific VDW and electrical forces by a const
> (that are associated with certain atoms).
> Could anyone advise me how to do this code change?
> Thanks in advance,
> Best regards,
> Asaf
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