Re: [AMBER] Equilibration phase and RMSD

From: David A Case <>
Date: Thu, 11 Sep 2014 15:30:31 -0400

On Thu, Sep 11, 2014, Ibrahim Said wrote:

> The protein is a structural protein involved in the formation of dimer or
> tetramer or octamer complexes with the protein or other proteins. For
> heating stage (200 ps), the RMSD became 20 A and then after equilibrtion
> the RMSD increased to 50 A. I calculated the RMSD using the minimized
> structure as the reference. please find the RMSD plot as attached file.

I agree with Carlos: visualization is your friend here. Are you sure you are
not including water molecules in the RMSD calculation?


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Received on Thu Sep 11 2014 - 13:00:03 PDT
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