VMD-L Mailing List

From: Mehdi Bagherpour (mehdi.bpour_at_gmail.com)
Date: Mon Feb 13 2017 - 11:32:53 CST

Dear VMD users:

I am going to use the adaptive biasing sampling (ABF) for getting free
energy landscape of protein-DNA affinity. For this reason I am going to
pull the protein along the helical axis as the protein always stays on
major groove. In fact, while protein moves along DNA helical axis,
simultaneously there is a rotation along this axis that keep protein on
major groove.

Question is, does anybody has a suggestion how can I choose the collective
variables?

Cheers,
Mahdi