> Date: Fri, 27 Mar 2009 09:56:02 +1100
> From: mark.abra...@anu.edu.au
> To: gmx-users@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:
src/gmxlib/nonbonded/nb_generic.c
which are easy to modify.
You will need to set the env var GMX_NB_GENERIC to use them.
Berk
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