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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 09 2020 - 05:30:03 PDT
