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.
Shuangxing Dai
----- Original Message -----
From: "Mark Abraham" <[email protected]>
To: "Discussion list for GROMACS users" <[email protected]>
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.
Mark
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
