Thank you for your reply,
But I have tried 'autoimage origin' as well and the results were same.
Actually I am simulating the permeability of a small molecule through lipid
bilayer. Molecules from adjacent periodic cells appear in few frames and
then disappear again. I have gone through a lot of literature but nothing
solid has been given anywhere.
On Thu 9 Jan, 2020, 5:43 PM Chetna Tyagi, <cheta231.gmail.com> wrote:
> 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,
> Chetna
>
> On Thu, Jan 9, 2020 at 12:58 PM Bhat Zahoor <dr.zahoor11.gmail.com> 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
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> Best wishes
> Chetna
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Received on Thu Jan 09 2020 - 05:30:02 PST
