Re: [AMBER] Lipid bilayer imaging problem

From: Chetna Tyagi <>
Date: Thu, 9 Jan 2020 12:48:47 +0100

Dear Zahoor,

Yes, that can happen...Try using "autoimage origin" before you trajout the
trajectory, if you haven't tried this way yet or "unwrapping" the
trajectory may also help sometimes.

unwrap [center] [{bymol | byres | byatom}] [ reference | ref <name> |
refindex <#> ] [<mask>]

If you have already tried these then I don't know further.
Many times with my membrane simulations, the lipids from adjacent cells
appear even after autoimaging but after few frames it goes back.

Hope it helps,

On Thu, Jan 9, 2020 at 12:58 PM 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
> _______________________________________________
> AMBER mailing list

Best wishes
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Received on Thu Jan 09 2020 - 04:30:02 PST
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