NetworkView plugin for the non-namd trajectories

From: James Starlight (
Date: Tue Apr 14 2015 - 09:34:57 CDT

Dear NAMD users!

I wonder to ask whether someone used VMDs NetworkView plugin for the
analysis of the biosimulations carried out not in NAMD (e,g I'm
working with Amber outputs now)? From the tutorial
I've found that to calculate covariance matrix prior to Networks
calculations some external programs like CARMA are used which directly
works with the NAMD-like psf topologies. Are there any other
possibilities to do the same using amber-like inputs topology assuming
that my trajectory has been converted in DCD? Is it possible to use
covariance matrix calculated by means of another software e,g g_covar?
What are the sequence of the steps will be in that case while loading
it's into VMD?


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