[AMBER] Strange RMSD tower appearing in simulation

From: Jorge da Rocha <jdarocha1.gmail.com>
Date: Tue, 8 Sep 2020 17:42:51 +0200

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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(image/png attachment: md_290ns_strange_spike.png)

Received on Tue Sep 08 2020 - 09:00:02 PDT
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