----- 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.
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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