[gmx-users] Shift Electrostatic Summation
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
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
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