Re: [AMBER] Question about RMSD "jumps"

From: Bill Ross <>
Date: Sat, 27 May 2017 17:48:05 -0700

Reimaging is the word. Maybe this older post still applies: "The cpptraj
'autoimage' was designed specifically to make this re-imaging easy."


On 5/27/17 4:26 PM, Ly, Thu Ngoc Anh wrote:
> Hello,
> 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!
> Regards,
> --
> 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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Received on Sat May 27 2017 - 18:00:03 PDT
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