VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Aug 28 2014 - 16:42:54 CDT

The APBS plugin in VMD is primarily meant as an easy-to-use interface
for APBS that helps reduce the need to hand-write APBS input files.
The details of the individual APBS parameters are described in the APBS
documentation and tutorials, and to do special calculations, you're best
off becoming familiar with those parameters from the APBS documentation itself:
  http://www.poissonboltzmann.org/

Cheers,
  John

On Thu, Aug 28, 2014 at 11:35:56PM +0200, Jean-Patrick Francoia wrote:
> Hello,
>
> I would like to draw a basic potential map on a molecule I created and
> "minimized" with Spartan (an octapeptide of lysine). The minimization in
> Spartan takes in account bonds angles and lengths, and charges. It is
> supposed to be basic, and done in vacuum.
>
> So now I'm trying to use the APBS plugin. My first shots were
> successful, I can use it and draw a potential map. The thing is there
> are plenty of parameters in the ELEC window.
>
> One for example: Dielectric constants.
> The solvent dielectric constant is set to 78.54 for example, but I would
> it to be set to 0, since I want to do everything in vacuum. Also, what
> is the solute dielectric constant ?
>
> So, could you give me a short explanation about the parameters I don't
> understand please ?
>
> Like:
>
> - Boundary condition
> - Vacc sphere density
> - Solvent radius
> - Spline window
> - System temperature (does it really matter in vacuum ?)
> - Surface tension
>
> I assume solvent radius and surface tension are parameters used to
> define a sphere of solvent, if we want to perform the simulation in
> solvent, right ?
>
> Thank you very much
>
> Sincerely 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/