From: Ashkan Shekaari (shekaari_at_email.kntu.ac.ir)
Date: Fri Sep 24 2021 - 15:53:23 CDT
constant force or constant velocity?
If constant velocity protocol is adopted, then increase pulling velocity.
---
,Best
Ashkan Shekaari
PhD Candidate in Solid State Physics
Department of Physics
K. N. Toosi University of Technology, Tehran, 15875-4416, Iran [ mailto:shekaari_at_email.kntu.ac.ir ] [ https://urldefense.com/v3/__https://scholar.google.com/citations?hl=en&user=LDzbXB4AAAAJ&view_op=list_works&sortby=pubdate__;!!DZ3fjg!t47dQSVQ7MXPuxhbjW-aUvgB7uxQWxFC0gb7e1XnTZP47O1E-o_9RVjJljMn5dQRcQ$ ]
From: "Ishaan Roy" <royi_at_uchicago.edu>
To: "namd-l" <namd-l_at_ks.uiuc.edu>
Sent: Friday, September 24, 2021 8:31:20 PM
Subject: namd-l: SMD in lipid
Hello,
I am trying to run SMD on a dimerized protein in a lipid membrane. However, with my current settings, the lipid stretches in the direction the protein is pulled (flexibleCell is on) and thins out in the middle. How can I prevent this from occurring?
Thanks,
Ishaan
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