Yes, but I still cannot write out the pair interaction for each ion since
there is cut off. With cut off, I need to assign a averge value of the last
two constants to each ion. But I cannot get the total number of neighbours
in a cut off distance in advance. So I cannot use the user defined part to
do my eletrostatic summation.
I compared carefully with Wolf summation with the Ewald summation, the
differences are:
1. There is no reciprocal term in Wolf.
2.Instead, the Wolf assums that the ions out side the truncations sphere is
exactly located at the sphere. That is how the extra two terms come out.
3. Wolf uses cut-off, while Ewald can only deal with peoriodical boundary
conditions cases.
So I need to add a similiar summation like Ewald to treat with the
long-range electrostatic force, not a non-bonded interaction. Then which
parts needs to be read and modified?
Thank you for your kindly help.
Shuangxing Dai
- Original Message -
From: "Mark Abraham"
To: "Discussion list for GROMACS users"
Sent: 26 March, 2009 4:56 PM
Subject: Re: [gmx-users] How to add another electrostatic summation methodin
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
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