[gmx-users] How to add another electrostatic summation methodinGromacs
Shuangxing Dai
shuangxingdai at gmail.com
Sat Mar 28 01:16:37 CET 2009
----- Original Message -----
From: "Mark Abraham" <Mark.Abraham at anu.edu.au>
To: "Discussion list for GROMACS users" <gmx-users at 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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