[gmx-users] How to add another electrostatic summation method in Gromacs

Berk Hess gmx3 at hotmail.com
Fri Mar 27 05:30:50 CET 2009

> Date: Fri, 27 Mar 2009 09:56:02 +1100
> From: Mark.Abraham at anu.edu.au
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] How to add another electrostatic summation method	in	Gromacs
> Shuangxing Dai wrote:
> > Thank you for your help. I attached the page of the form of potential. 
> > The equation (5.13) gives all the potential energy of neighbours of one 
> > ion in a truncation sphere.  Rc is cut-off. Since this potential depends 
> > on all the neighbours in a cut-off distance, I cannot give the pair 
> > interaction because in this method, only the total potential energy of 
> > one ion maks sense. In Ewald summation, both the real space and 
> > reciprocal space summation can be written as the summation of pair 
> > potential. But in wolf, I cannot do that.
> It looks separable into a double sum over atom pairs from within a 
> cutoff, since the value of that limit is constant.
> > Since I cannot use Ewald without peoriodical boundary conditions while 
> > this Wolf method can, so I cannot simply use Gromacs to do my 
> > simulation. The question is which files needed to be modified if I want 
> > to add a new one? Is there any direct way? Or I should read all the 
> > whole code?
> You can start by reading the kernel code generated by mknb during the 
> make process and found in src/gmxlib/nonbonded/nb_kernel. If you play 
> with the flags to mknb you can get comments embedded in the C files. 
> Find the one that does Ewald without table lookups and consider how 
> you'd need to change it to suit your needs.
> Mark

Note that in 4.0 there are now also plain c loops:
which are easy to modify.
You will need to set the env var GMX_NB_GENERIC to use them.


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