Re: SMD in lipid

From: Ashkan Shekaari (
Date: Fri Sep 24 2021 - 15:53:23 CDT

constant force or constant velocity?
If constant velocity protocol is adopted, then increase pulling velocity.

Ashkan Shekaari
PhD Candidate in Solid State Physics
Department of Physics
K. N. Toosi University of Technology, Tehran, 15875-4416, Iran [ ] [;!!DZ3fjg!t47dQSVQ7MXPuxhbjW-aUvgB7uxQWxFC0gb7e1XnTZP47O1E-o_9RVjJljMn5dQRcQ$ ]

From: "Ishaan Roy" <>
To: "namd-l" <>
Sent: Friday, September 24, 2021 8:31:20 PM
Subject: namd-l: SMD in lipid


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?



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