From: McGuire, Kelly (
Date: Wed Jul 18 2018 - 19:18:34 CDT

This might be a question for the NAMD mailing list as well. I have a homotetramer ion channel in a lipid bilayer, and each peptide of this channel is completely alpha helical. Sometimes after I minimize, or anneal, or equilibrate, or even at my ABF step of the simulation I'll notice parts of the alpha helices (new cartoon representation) becoming more like the tube representation. During minimization, annealing, and equilibration there is a backbone restraint on the protein (none on the bilayer, water, or ions), and then at the ABF step, all restraints are off. What could be some of the causes for alpha helices in the new cartoon representation to shift toward more tube like representations?

Kelly L. McGuire

PhD Scholar


Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602