[gmx-users] How to add another electrostatic summation methodin Gromacs
shuangxingdai at gmail.com
Fri Mar 27 21:20:09 CET 2009
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
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
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.
----- Original Message -----
From: "Mark Abraham" <Mark.Abraham at anu.edu.au>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: 26 March, 2009 4:56 PM
Subject: Re: [gmx-users] How to add another electrostatic summation methodin
> 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.
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