Steered MD along detected routes

From: Johny Telecaster (
Date: Sat Nov 16 2013 - 05:10:40 CST

Dear NAMD Developers,

I have some questions about stereed MD. In particular I'd like to simulate
ligand unbinding from the enzyme. Using CAVER Pymol plugin I've detected 3
possible paths inside my protein. Now I'd like to run stereed MD along each
of that routes to measure forces affected on the ligand during its motions
along each of it. How I could define force directions presicely along
CAVER paths? Does it possible to define this pathes as the colvar
restrictions? Please provide me with example.

Many thanks for the suggestions,

Johny T.

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