[gmx-users] Shift Electrostatic Summation
shuangxingdai at gmail.com
Wed Apr 15 03:35:07 CEST 2009
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.
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?
Thank you for your help.
----- 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 12:46 AM
Subject: Re: [gmx-users] Shift Electrostatic Summation
> Shuangxing Dai wrote:
>> Hi, all,
>> I was wondering to modify Shift electrostatic summation to a new one.
>> The origin Shift form in Gromacs is like 1/r-1/Rc (Rc is cut-off), I need
>> to modify to erfc(alpha*r)/r-erfc(alpha*Rc)/Rc, and the original
>> long-range correction of Shift in code shift_util.c is q^2/(2*Rc) (
>> something like that ), I need to
>> q^2*(erfc(alpha*Rc)/(2*Rc)+alpha/sqrt(pi)). So question is:
>> How the force to Shift was calculated? Gromacs use the differentiation to
>> energy, got the force formula, then calculated the force? Or just use the
>> numerical differentiation to the energy and got it? If is the latter one,
>> I do not need to modify the force calculation.
> GROMACS uses exclusively analytic rather than numerical forces. Probably
> table lookups as used for PME are the technique you will want to
> implement. You won't need to change any code if your functions are
> suitably continuous functions of r and constant parameters. See the
> tabulated potentials section in the manual.
>> And also, the alpha for Ewald summation, is there an option or parameters
>> to adjust this value?
> Yes - see the Ewald section of the manual. Also search the mailing list,
> as this has been discussed several times.
>> Hi, Mark and Berk, if I want do modify shift electrostatic summation as I
>> want, what other files or place do I need to modify, except shift_util.c
>> and force.c?
> Don't - use table lookups.
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