VMD-L Mailing List

From: Cesar Luis Avila (cavila_at_fbqf.unt.edu.ar)
Date: Tue Jun 12 2007 - 11:22:26 CDT

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
>