[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 

> 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 
 Thank you for your kind help.
> Mark
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