VMD-L Mailing List

From: Fotis Baltoumas (fbaltoumas_at_biol.uoa.gr)
Date: Tue Aug 26 2014 - 10:39:47 CDT

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