VMD-L Mailing List

From: Cesar Luis Avila (cavila_at_fbqf.unt.edu.ar)
Date: Tue Jun 12 2007 - 11:18:47 CDT

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