Re: [AMBER] rmsd plot error

From: Saman Yousuf ali <>
Date: Fri, 8 Jul 2016 12:28:28 +0000 (UTC)

Dear vlad,
Thank you for your help. My rmsd y-axis is in angstrom. I have run backbone atoms rmsd. Script is pasted below.
rms first :1-526.CA,C,N out rmsd-tac.dat
atomicfluct out rmsf-tac.dat :1-526.CA,C,N byres
strip :WAT
strip :Cl-
 Best Regards, Saman Yousuf AliJunior Research Fellow,
| Lab No. P-133, Computational Chemistry Laboratory
Dr. Panjwani Center for Molecular Medicine & Drug Research,
International Center for Chemical & Biological Sciences,
University of Karachi – 75270.Karachi-Pakistan.

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    On Friday, July 8, 2016 5:17 AM, Vlad Cojocaru <> wrote:

  This looks to me like an imaging issue with that frame (or those few frames) .... check the frame(s), you should be able to see in a visualization software what happens. If it is an imaging issue, simply remove it (them) from the processed trajectory.... If for some reason you really need exactly those frames affected, try some manual imaging procedures ... or re-run the simulation (5 ns should be doable)
 Just a remark ...  if your y axis is nm, the rmsd looks to quite large during the entire simulation.... How did you calculate the RMSD ? What parts of the system did you fit ? Is this RMSD for the fitted parts or for other parts ?
 On 07/08/2016 01:42 PM, Saman Yousuf ali wrote:
 Dear zoran,
This rmsd plot is generated after 5ns production run. I have performed protein ligand complex md simulation. When I reimaged my mdcrd after production it gives me following error for 1ns trajectory; Warning: autoimage: Frame 20 imaging failed, box lengths are zero. While rest of proceed normally without this warning. you see in attached file that the rmsd jumps to near20 angstroms. This is a sign of something seriouslywrong with the trajectory. 
 Best Regards, Sarah

    On Friday, July 8, 2016 4:17 AM, zoran matovic <> wrote:

What kind of MD (heating, equil., production)? What kind of molecule is the
"complex"? What was the reference structure you have used for RMSD? What's
up to me you have nice equilibrium after 5 ns.


Dear all,
I have performed 5ns md simulation using amber14. Rmsd plot of one my
simulated complex shows unusua 20 angstrom fluctuation at starting ns. I am
unable to understand the reason. Rmsd plot is attached below. Kindly help
me. Best Regards, Sarah

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Dr. Vlad Cojocaru
Computational Structural Biology Laboratory
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]

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Received on Fri Jul 08 2016 - 05:30:03 PDT
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