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.
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?
This is because we use tables internally for this as well. The tables
are generated in tables.c.
However you may want to look at the self energy correction routines for
shift functions (I think it is called shift_util.c).
Decomposing energy is a very tricky business, and in most cases does not
give you any meaningful results.
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
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