If you are not using the iwrap = 1 feature, don't start now!
It is perplexing if this is NOT your issue--because your visualization is
exactly what we'd expect to see if iwrap = 1 and there is nothing else I
can think of that would cause this behavior.
Dave
On Wed, Sep 9, 2020 at 8:09 AM Jorge da Rocha <jdarocha1.gmail.com> wrote:
> Dear Amber Helpers,
>
> Thank you for the suggestions and advice!
>
> We are not using the iwrap function - but we will try to if we
> don't succeed on correcting the imaging.
>
> Here is a visualization of the section with the spike, it looks like part
> of the structure moves over to the next periodic box.
>
> https://we.tl/t-b9BQ77u7y2
>
> This is what Dr Anselm has described, so we will try to "unwrap" in cpptraj
> - we aren't sure if this will work due to us not having used the iwrap
> function to begin with.
>
> Any advice or suggestions are always welcome, and we'll post updates soon.
>
> Thank you all!
> Warm regards
> Jorge
>
> On Tue, 8 Sep 2020 at 17:42, Jorge da Rocha <jdarocha1.gmail.com> wrote:
>
> > Dear Amber Users,
> >
> > I am running a simulation of a large homodimeric protein (15800 atoms).
> > The simulation mostly runs well, but a large tower/spike of RMSD around
> > 240ns.
> >
> > I have tried to address the artefact by using autoimage, and anchoring to
> > the residues of the structure, but the issue persists.
> >
> > I am using pmemd.cuda for the simulation.
> >
> > Have you any advice of how to resolve this, or ideas of what could be
> > causing this? I will be rerunning that section of simulation in the mean
> > time to see if anything changes.
> >
> > Warm Regards
> > Jorge da Rocha
> > --
> > Jorge da Rocha (MSc Med)
> > PhD Candidate at the Sydney Brenner Institute for Molecular Bioscience
> > Division of Human Genetics, Faculty of Health Sciences
> > University of the Witwatersrand
> > Cell: 082 944 1651
> >
>
>
> --
> Jorge da Rocha (MSc Med)
> PhD Candidate at the Sydney Brenner Institute for Molecular Bioscience
> Division of Human Genetics, Faculty of Health Sciences
> University of the Witwatersrand
> Cell: 082 944 1651
> _______________________________________________
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> AMBER.ambermd.org
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>
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Received on Wed Sep 09 2020 - 08:30:02 PDT
