Shuangxing Dai wrote:
----- 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.
So the "total number of neighbours in a cut off distance" doesn't seem
to enter the expression...
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.
Sure
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?
Such a summation method is algorithmically a short-range interaction,
not a long-range one (like a reaction-field contribution, or a mesh
contribution from PME or PPPM), which is the reason I didn't understand
your conclusion above.
Like I said a day or two back, the nonbonded kernels do the real-space
summation for Ewald. For speed, in the optimized kernels the
erfc(alpha*r)/r bit is pre-computed in a table and looked up. Hence
wanting to cast your expression to use the same trick.
Mark
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