[AMBER] Structure Artifact After Autoimage

From: Mikhael, Simoun <Simoun.Mikhael.cshs.org>
Date: Fri, 31 Jul 2020 21:01:52 +0000


I use autoimage to center the trajectories of the water box and protein (pentamer) structure. However, I get an artifact that isn't present before I do the autoimage.
I've attached an image to show the artifact where some of the atoms are flying around the protein structure. Do you know what could be the reason, and how to fix that artifact?
I use the following commnds:

> parm protein.prmtop
> trajin protein_step6.nc 1 500 10
> autoimage
> trajout autoimage_protein.mdcrd mdcrd
> run


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(image/png attachment: after_autoimage.PNG)

Received on Fri Jul 31 2020 - 14:30:03 PDT
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