VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Oct 31 2009 - 14:42:05 CDT

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On Wed, 2009-10-28 at 12:54 -0400, Christine Horejs wrote:
> Dear all,

dear christine,

> I was using the RBCG tool to coarse-grain a protein. Does anyone know,
> what the diameters of the beads are? Are they calculated from the vdW

from looking at the tcl script code: what you see on the screen,
the radii are just what VMD guesses from the generated .pdb file
times a factor of 2.

> volume by assuming a spherical shape for the individual residues?

the mode is using 12-6 LJ interactions, so of course the residues
are built from spherical beads.

cheers,
    axel.

>
> Thank you for your help,
> Christine

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com 
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.

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