Re: SMD on Intermembrane Helices

From: Ashkan Shekaari (
Date: Tue Dec 22 2020 - 11:32:32 CST

I mean stretching a system would necessarily impose conformational changes.

All the best, 
Ashkan Shekaari, 
Ph.D Candidate in Solid State Physics, 
K. N. Toosi University of Technology, 
Tehran, Iran 
From: "Ethan Croitoru" <> 
To: "namd-l" <> 
Sent: Tuesday, December 22, 2020 8:45:45 PM 
Subject: namd-l: SMD on Intermembrane Helices 
Hi everyone, 
I am trying to run an SMD simulation separating two helices in a membrane. I am doing this for free energy calculations, so I am using colvars to sample the conformations as they separate. To pull them apart I used a harmonic on the distance colvar with a forceConstant of 5. However, in my simulations the helices become disfigured and there is a kink in the middle. I was wondering if anyone had suggestions as how to pull the helices apart without them morphing. 
Thank you for the help, 
Ethan Croitoru 

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