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

[Christoph Junghans]

2013/8/30 Asaf Farhi <asaf.farhi at weizmann.ac.il>:
> 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?
The problem is basically that for particle pairs with a distance
bigger than the cutoff distance, forces nor energies are calculated
and hence have contribution 0. You could do a simulation with an
infinite cutoff, which is what the allvsall kernel does.
You would need to modify src/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.c

>
> 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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>
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-- 
Christoph Junghans
Web: http://www.compphys.de