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

[Asaf Farhi]

Dear Prof. Shirts

Thank you very much for the response and for telling me where the code is. 
Could you please explain in more detail the energy conservation? - why is it not conserved? and if so why is it problematic?

Thanks in advance,
Best regards,
Asaf

p.s the method has also other aspects that can be read. I hope that you'll find them interesting.
________________________________________
From: gmx-developers-bounces at gromacs.org [gmx-developers-bounces at gromacs.org] on behalf of Shirts, Michael (mrs5pt) [mrs5pt at eservices.virginia.edu]
Sent: Friday, August 30, 2013 3:39 PM
To: Discussion list for GROMACS development
Subject: Re: [gmx-developers] editing the code of the VDW and electric  potentials and forces

Note that this looks fairly similar to:

http://dx.doi.org/10.1002/jcc.21938

The relevant code would be in:
src/gmxlib/nonbonded/nb_free_energy.c

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
conservation.

Best,
~~~~~~~~~~~~
Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu
(434)-243-1821


> 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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