----- Original Message -----
From: "Mark Abraham" <mark.abra...@anu.edu.au>
To: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Sent: 27 March, 2009 5:01 PM
Subject: Re: [gmx-users] How to add another electrostatic summation
methodinGromacs
Shuangxing Dai wrote:
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.
If N is the number of neighbours inside the cutoff distance, then you
might be right. If so, then I don't understand why the inner summation
constrains "j != i" and "r_ij < R_c" since the latter is implied by
formation of the set over which the summations are occurring.
If N is the total number of ions then the last few terms are all
system-wide constants.
Sorry, (5.13) is the total electrostatic potential energy for the system
and the N is the total number of ions.
I also don't understand why the limit expression exists. For any values
actually used in a simulation, that expression is just a constant.
In simulation, we simply uses r_ij = R_c, so ignore the limit.
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.
The second and third terms came from this treatment.
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?
I don't understand your conclusion, here.
OK. I mean I need to add a eletrostatic summation method very similiar to
Ewald. So where is definition/algorithm of Ewald in Gromacs and how to add
one?
Thank you for your kind help.
Mark
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