[AMBER] Lipid bilayer imaging problem

From: Bhat Zahoor <dr.zahoor11.gmail.com>
Date: Thu, 9 Jan 2020 17:28:07 +0530


I have simulated DOPC lipid bilayer model ( Explicit solvent) for 100ns
using Lipid14 force field in Amber18. Now I was trying to process the
trajectory file using autoimage flag in the CPPTRAJ and keeping center
residues of my choice. But it appears that the adjacent cell lipid
molecules appear in the simulation unit cell when visualized in the VMD.
Although I have used Periodic boundary condition while running the
production run and simulated the system in NPT ensemble. I have been trying
to image the trajectory using different options as reported earlier in the
amber mail archive. I have solved the water layer shifting problem but the
lateral lipid molecules from the adjacent periodic images appear in the
unit cell. What would be the cause and the possible solution for this
problem ?

*Zahoor Ahmad Bhat*
Research Scholar
Multidisciplinary Centre for Advanced Research and Studies
Jamia Millia Islamia
New Delhi - 110025
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Received on Thu Jan 09 2020 - 04:00:02 PST
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