VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jun 12 2007 - 16:48:54 CDT

Hi,
  Yes, the pmepot plugin will use the charges set in the PSF.
You'll want to read the plugin documentation page for pmepot, which
includes links to references that give further details about the method:
  http://www.ks.uiuc.edu/Research/vmd/plugins/pmepot/

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jun 12, 2007 at 01:22:26PM -0300, Cesar Luis Avila wrote:
> I have the psf and dcd (100 frames) for the whole system loaded into
> vmd. Does PME automatically take the charges from this files?
>
> Cesar Luis Avila escribió:
> >Dear all,
> >I was wondering if there is a tutorial available for PME plugin
> >calculation and visualization. I would like to calculate and represent
> >Isosurface electrostatic potential from a trajectory for a protein.
> >Then I will be able to compare the results to the ones obtained from a
> >static picture, as those obtained with APBS using implicit solvent.
> >
> >At least I would need two tips,
> >1- In PME calculation, should I select the whole system (protein +
> >water + ions) or just the protein ?
> >2- Which values should I use to represent +/- 25 mV isosurfaces? ( I
> >suppose +/- 1, is this correct) ?
> >
> >Regards
> >
> >Cesar
> > 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078