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" <[email protected]>
To: "Discussion list for GROMACS users" <[email protected]>
Sent: 14 April, 2009 10:21 PM
Subject: Re: [gmx-users] Shift Electrostatic Summation
Shuangxing Dai wrote:
----- Original Message ----- From: "Mark Abraham"
<[email protected]>
To: "Discussion list for GROMACS users" <[email protected]>
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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