From: Kirby Vandivort (
Date: Tue Aug 26 2014 - 10:53:27 CDT


These values are used in the code when getting the adjacency matrix. If you
look in adjacencyMatrix.tcl, there are two values near the top:

     variable distanceCutoff 4.5
     variable requiredOccupancy 0.75

That should be what you need.


On 08/26/2014 10:39 AM, Fotis Baltoumas wrote:
> Dear VMD mailing list,
> In the Dynamical Network Analysis tutorial, it is stated that edges are
> drawn between nodes whose residues are within a cutoff distance (4.5
> Angs.) for at least 75% of an MD trajectory. If atoms corresponding to a
> node (n1) are within the contact distance of atoms from another node (n2)
> for 75% of the trajectory, then the pairwise (n1,n2) correlation is kept,
> and an edge will be created between n1 and n2 in the network.
> How are these cutoff values (4.5 and 75%) defined during the creation of
> the network? They are not present in the network.config file, which is
> used to prepare the network. I also checked the networkSetup.tcl script of
> the NetworkView plugin, which is used in the tutorial and I couldn't find
> anything relevant. Therefore, what would I have to tweak or edit if I
> wanted to change these values (to say, 5.0 angstroms and 90% of the
> trajectory)?
> Thank you in advance,
> Fotis Baltoumas

Kirby Vandivort                      Theoretical and
Senior Research Programmer            Computational Biophysics
Email:          3061 Beckman Institute    University of Illinois
Phone: (217) 244-5711                405 N. Mathews Ave
Fax  : (217) 244-6078                Urbana, IL  61801, USA