VMD-L Mailing List

From: amin sagar (aamin.sagar_at_gmail.com)
Date: Sat Aug 18 2018 - 13:13:41 CDT

Dear All,
I am doing Dynamic Network Analysis on my protein-protein complex after an
SMD simulation. I am finding that sometimes the path backtraces i.e. it
goes back to the same node and then goes in a different direction. For
example, this is suboptimal path 1
206, *204, 117, 204*, 202, 200, 114, 112, 110, 108, 135, 137, 101, 227,
320, 299, 323, 325, 366, 364, 332, 334, 338, 438, 440
Notice, it goes from 204 to 117 and then back to 204.
This seems strange to me. Has anyone else experienced this and is this
expected?
My system selection has all the atoms of two protein chains and the nodes
are just C alpha atoms.
I would really appreciate any suggestions.

Best,
Amin.