[AMBER] Adjacent cell molecules appear in the trajectory after autoimaging in cpptraj [ DOPC lipid bilayer simulation with lipid14 force field]

From: Bhat Zahoor <dr.zahoor11.gmail.com>
Date: Wed, 8 Jan 2020 15:16:26 +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 trajectory when visualized in the VMD. Although I
have used Periodic boundary condition while running the production run and
simulated the system in NPT ensemble. 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 Wed Jan 08 2020 - 02:00:02 PST
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