[gmx-users] Shift Electrostatic Summation

David van der Spoel spoel at xray.bmc.uu.se
Tue Apr 14 08:40:03 CEST 2009

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.
> And also, the alpha for Ewald summation, is there an option or 
> parameters to adjust this value?
> 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?
> Shuangxing Dai

It would be wise to test everything with a table look up. Much easier, 
and the better performance than analytical potentials.

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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

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