[gmx-users] Shift Electrostatic Summation

Shuangxing Dai shuangxingdai at gmail.com
Wed Apr 15 04:33:44 CEST 2009

----- Original Message ----- 
From: "Mark Abraham" <Mark.Abraham at anu.edu.au>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: 14 April, 2009 8:01 PM
Subject: Re: [gmx-users] Shift Electrostatic Summation

> Shuangxing Dai wrote:
>> Thank you for your help. Yes, when I found the user define part for 
>> electrostatics, I hope I can use this part since the analytic form of my 
>> potential is known. However, since there is a self energy term exist and 
>> then the whole energy cannot be decomposed to pair interactions because I 
>> cannot specify how much to each pair since the number of neighbours is 
>> unkown. That is why I am confused. So I still need an new electrostatic 
>> summation similiar to shift, not just a new pair interaction.
> The number of neighbours is known at run-time. However, I still don't see 
> why this matters - see 
> http://www.gromacs.org/pipermail/gmx-users/2009-March/040830.html
OK, the self energy is assigned for each ion. If I want to decompose the 
potential form of total energy to summation of pair potential, I should 
devide the self term by number of neighbours and assigned to each pair. So I 
cannot use user define potential for my problem.

>> And I cannot understand/find how the force for Shift electrostatic 
>> summation is calculated in force.c since there is no formula for force 
>> found. Or I find the wrong place? And if I want to modify the force 
>> formula for Shift, where is it?
> Look in the nonbonded kernels - like I said in the above post and 
> previously.
> Mark
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