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
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