[gmx-users] Shift Electrostatic Summation
David van der Spoel
spoel at xray.bmc.uu.se
Wed Apr 15 07:37:20 CEST 2009
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" <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
>> 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.
>> gmx-users mailing list gmx-users at gromacs.org
>> Please search the archive at http://www.gromacs.org/search before
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> gmx-users mailing list gmx-users at gromacs.org
> 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
More information about the gromacs.org_gmx-users