From: Vlad Cojocaru (
Date: Sat Dec 13 2014 - 06:40:55 CST

Dear all,

I encountered a problem with the network view plugin ....

I performed a dynamic network analysis and at the last stage I run
"subopt" to calculate the pathways between 2 nodes in the network. To
run subopt I used the index number of the 2 nodes from the "carma.psf"
file that was generated in the first stage from the original all-atom
psf file ...

Then I used the original all-atom PSF file to visualize the pathways
using the NetworkView plugin. However, I noticed the when I calculate
paths between nodes of lets say residue 100 and 200, the networkView
plugin draws the paths between residues 101 and 201 (only one network
node per residue) ...

I thought that the output of subopt is according to the "carma.psf" file
and this will be translated to the correct indices in the original
all-atom PSF, of course taking into account that when visualizing, VMD
will actually count from 0

Did anybody notice this behavior ? Is this a bug in the plugin or am I
missing something here ?

Best wishes

Dr. Vlad Cojocaru
Computational Structural Biology Laboratory
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]