From: Ashkan Shekaari (shekaari_at_email.kntu.ac.ir)
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" <ecroitoru1_at_gmail.com> To: "namd-l" <namd-l_at_ks.uiuc.edu> 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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