Re: [AMBER] PROTEIN-DNA rmsd plot

From: David A Case <>
Date: Mon, 21 Dec 2020 08:12:57 -0500

On Mon, Dec 21, 2020, Syeda Amna Arshi wrote:

>I think that my complex has been moving out of the octahedron water box
>(TIP3PBOX) during the simulation, it looks like part of the complex goes
>out of the box at many points.

This is expected: the complex is just drifting into a neighboring unit
cell. See the autoimage command in cpptraj, which will pack molecules
back into a single unit cell, making it easier to visualize.


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Received on Mon Dec 21 2020 - 05:30:02 PST
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