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

Asaf Farhi asaf.farhi at weizmann.ac.il
Fri Aug 30 09:35:46 CEST 2013

Dear Dr. Feenstra K.A

Thank you very much for your response.

What I'm trying to achieve is explained at:

In short, if it is combined with multiplication by lambda=[0,1] it is supposed to come instead of the chance in the VDW and electric potential that is associated with "annihilation". If Ec will have value of around 7kCal/mole I think that it should have negligible effect on the free energy at lambda=1.

Do you know if it is explained in the manual also how to multiply VDW and electric forces (that are associated with certian atoms) by a const ?

Thanks again,
Best regards,

From: gmx-developers-bounces at gromacs.org [gmx-developers-bounces at gromacs.org] on behalf of Feenstra, K.A. [k.a.feenstra at vu.nl]
Sent: Friday, August 30, 2013 10:02 AM
To: Discussion list for GROMACS development
Cc: Discussion list for GROMACS development
Subject: Re: [gmx-developers] editing the code of the VDW and electric potentials and forces

Op 30 aug. 2013 om 08:49 heeft "Asaf Farhi" <asaf.farhi at weizmann.ac.il<mailto:asaf.farhi at weizmann.ac.il>> het volgende geschreven:

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)
If (E_EL>Ec)

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?

If I understand what you want to do, i.e. a fixed upper limit to the energies, than you could do that easily, without touching the code, bu using interaction tables. You will find how in the manual.

What you haven't explained is what you want to achieve.

The setup you describe will give an unphysical discontinuity in the forces, which will give rise to some strange artifacts in your simulations for sure. I expect these may be similar, in type and severity, to those associated with the simple interaction cut-off schemes. Using that as a basis for 'a novel free energy calculation method' seems rather unlikely to produce valid results.

Thanks in advance,
Best regards,
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