Re: [AMBER] Strange RMSD tower appearing in simulation

From: David A Case <>
Date: Tue, 8 Sep 2020 14:23:42 -0400

On Tue, Sep 08, 2020, Dave Cerutti wrote:

>Yes, this looks like an imaging problem--if you have iwrap = 1 in your
>&cntrl, the homoDIMERIC protein is two molecules, so each will be re-imaged

Everyone wants to chime in on this one!

It would be good to know if you are indeed using iwrap=1. If so, you
see a reaoson to avoid that in the future.

You *should* be able to undo the wrapping in cpptraj, and get a proper
RMS vs. time plot, without having to re-run any of the simulation.
Check out the "unwrap" option in cpptraj.

[This all assumes that this is indeed a wrapping problem -- as Carlos
suggests, visualization is your friend here.]


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Received on Tue Sep 08 2020 - 11:30:03 PDT
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