[Chimera-users] Coulombic Potential Dielectric

[Elaine Meng]

Hi Nikolay,
Coulombic calculations do not use separate values of the dielectric for solvent and solute.  All the point charges are treated the same, and only the solute is considered.  The default dielectric is distance-dependent, and the 4 is just a multiplier (dielectric = 4r, where r is distance).   See Coulomb's law in the manual page:

http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic.html

Best,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jul 26, 2012, at 11:41 AM, Nikolay Igorovich Rodionov wrote:

>                 Hi, I just have a question about the default dielectric coefficient in the Coulombic surface coloring function. Does the coefficient of 4 correspond to the dielectric of the solvent or the solute (the biomolecule)? I think the latter makes more sense but I just want to make sure.
>  
> Thanks!
> Nikolay Rodionov
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users