VMD-L Mailing List
From: Jean-Patrick Francoia (jeanpatrick.francoia_at_gmail.com)
Date: Thu Aug 28 2014 - 16:35:56 CDT
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 ?
- 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