Did you visualize the trajectory? That will tell you if it is an imaging
problem or not ( most likely it is)
On Tue, Sep 8, 2020 at 11:43 AM 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
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Received on Tue Sep 08 2020 - 09:00:03 PDT
