[Chimera-users] Coulombic Potential Dielectric

[Nikolay Igorovich Rodionov]

Thanks!

-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: Thursday, July 26, 2012 3:03 PM
To: Nikolay Igorovich Rodionov
Cc: chimera-users at cgl.ucsf.edu BB
Subject: Re: [Chimera-users] Coulombic Potential Dielectric

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
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