[AMBER] Question about RMSD "jumps"

From: Ly, Thu Ngoc Anh <thu.ly.wsu.edu>
Date: Sat, 27 May 2017 23:26:55 +0000


I used Amber 11 to run simulations on two polypeptides. Each polypeptide is a dimer (coiled coil) and the only difference between them is that one has a mutation at residue 21 (R21H) while the other does not (wild-type). No ligand was involved. When I calculated the RMSD, I noticed the "jumps", so I recorded a movie for each simulation and saw that the two strands came apart at certain time points. Attached are scatter plots of RMSD calculations.

My questions are as follows:

  1. Is this purely an issue of periodic boundary conditions. If it is, what is the best way to correct it? I'm thinking to re-run each simulation with a bigger solvation box? The one I used was a 10-angstrom water box (the command line was: solvatebox xyz TIP3PBOX 10. 0.75)
  2. Despite the jumps, is it still correct to say that the peptides did reach pseudo-steady states? If so, can I just remove the jumps from the RMSD plots without re-running the simulations?

I really appreciate any help and/or suggestions!

Thu (Lily) Ly
Graduate Research Assistant
Gene and Linda Voiland School of Chemical Engineering and Bioengineering
Washington State University
Wegner Hall 334
Pullman WA 99164-6515
Mobile | 206.446.1768

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(image/png attachment: RMSDs.png)

Received on Sat May 27 2017 - 16:30:02 PDT
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