Re: [apbs-users] potental interpretation if epsilon_mol=epsilon_solvent

[<M.V...@lu...>]

Dear Nathan, 
I am simulating images in cryo-electron microscopy.  For a phantom (specimen) one needs to model the potential (incident electrons scatter against the total potential of the specimen).
Starting model of potential is calculated via electron scattering factors. However, this model assumes that atoms are isolated and I am combining it with APBS potential to account for the solvent and ions influence. 
For this I use of course heterogeneous minus homogenous dielectric calculations, but I thought that adding that homogenous model to include redistribution within the molecule can be beneficial. 
This practically means to perform only heterogeneous dielectric calculation (without subtraction)?
I understand that the accuracy of the calculated potential depends a lot on a way how partial charge delta peaks are treated. In the case of heterogeneous minus homogenous the singularities are at the same place so the final difference is smooth?

Do you think it will be beneficial for my model to use only heterogeneous model?
Is the easiest way to do it deleting the second part of a default .in file?
thanks a lot for the help
Milos


________________________________________
From: Baker, Nathan [Nat...@pn...]
Sent: Saturday, September 29, 2012 12:50 AM
To: Vulovic, M.V. (MCB); apb...@li...
Cc: apb...@go...
Subject: Re: [apbs-users] potental interpretation if epsilon_mol=epsilon_solvent

Hello --

It would provide a coarse electrostatics description inside the molecule but, if that's all you wanted, then you could just use Coulomb's law.  The most useful thing you can do with the results of the calculation you describe is to subtract it from the results of a heterogeneous dielectric calculation (e.g., solvent dialectic 80, solute dielectric 2).  The resulting potential will be the reaction field potential attributable to the polarization of the solvent around the solute.

Thanks,

--
Nathan Baker
Pacific Northwest National Laboratory
Tel:  +1-509-375-3997
http://nabaker.me


From: "M.V...@lu...<mailto:M.V...@lu...>" <M.V...@lu...<mailto:M.V...@lu...>>
Date: Friday, September 28, 2012 7:25 AM
To: APBS-USERS mailing list <apb...@li...<mailto:apb...@li...>>
Cc: APBS-USERS mailing list <apb...@go...<mailto:apb...@go...>>
Subject: [apbs-users] potental interpretation if epsilon_mol=epsilon_solvent

Dear,
how should I interpret the final potential that I got from APBS after setting the dielectric constant of the solvent equal to the dielectric constant of the solute =2?
Would this give me a course representation of the potential inside the molecule due to redistribution of the charges via e.g. covalent bonds (if initially AMBER force field is used in pdb2pqr)? Is this redistribution between a small groups of atoms (residues).
thank you a lot

M Vulovic

TU Delft/LUMC