Re: [AMBER] Lipid bilayer imaging problem

From: Daniel Roe <>
Date: Tue, 4 Aug 2020 10:29:01 -0400


Yeah, imaging bilayers can be tough. One option you could try is
'moveanchor' - once a molecule is imaged this uses the previous one as
an anchor. It might work for you.


On Thu, Jan 9, 2020 at 6:58 AM Bhat Zahoor <> wrote:
> Hello,
> 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 ?
> Thanks
> *Zahoor Ahmad Bhat*
> Research Scholar
> Multidisciplinary Centre for Advanced Research and Studies
> Jamia Millia Islamia
> New Delhi - 110025
> India
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Received on Tue Aug 04 2020 - 07:30:03 PDT
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