[gmx-users] Shift Electrostatic Summation

[Shuangxing Dai]

Thank you for your advice and sorry for the misinterpretation. The N is the 
total number of the system and E^Mad_tot is the total energy for the system. 
The outer loop sums over all the ions and the inner one sums over the 
neighbours in the cut-off radius. So it is difficult to decompose this total 
energy to the summation of pair potential since the self energy part is not 
easy to decompose.
I will follow your advice. Thanks again.
Shuangxing Dai
----- 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 10:21 PM
Subject: Re: [gmx-users] Shift Electrostatic Summation


> Shuangxing Dai wrote:
>>
>> ----- 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.
>
> You can use a user potential if the dependence of the force and/or 
> potential on r and N is sufficiently separable. The number of neighbours 
> is known inside the inner nonbonded loops, because they're looping over 
> the neighbours of each particle. So you merely do a table lookup before or 
> after some function of N is applied to some function of r. Thus the only 
> work you'd need to do is to construct the correct form of tables, and add 
> in the arithmetic concerning N.
>
> Per my advice in that previous thread, you should read and understand the 
> code for the nonbonded kernel for a straight cutoff, compare that with 
> non-table-lookup Ewald, and compare that with table-lookup Ewald. Also 
> heed the advice Berk gave you.
>
> You've still never explained why N in the formula in that previous thread 
> is the number of neighbours of a given particle, not the number of 
> particles in the system - but that's your problem.
>
> Mark
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