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

[Shirts, Michael (mrs5pt)]

> 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?

This is a fundamental principle in molecular dynamics -- the potential
energy and the force need to be consistent with each other.  Discontinuities
in the potential lead to infinite spikes in the force, which leads to lack
of energy conservation, which leads to the incorrect ensemble being sampled.
You may need to spend more time reading about molecular dynamics
fundamentals before you start changing code too much!

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>
> Date: Fri, 30 Aug 2013 16:30:08 +0000
> To: "michael.shirts at virginia.edu" <michael.shirts at virginia.edu>, Discussion
> list for GROMACS development <gmx-developers at gromacs.org>
> Subject: RE: [gmx-developers] editing the code of the VDW and electric
> potentials and forces
> 
> 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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