OK, sorry but you mentioned a jump to 20 Angstr whereas your plot shows
just 2 on the y axis. So I assumed you plot in nm .... If its a jump to
20 Angstr and you don't see it in the plot because you don't show the
full scale, its a typical imaging issue ... Did you visualize your
trajectory and go to the frame(s) that's causing problems ? How does it
look like ?? How many frames are affected ?
Best
Vlad
On 07/08/2016 02:28 PM, Saman Yousuf ali wrote:
> Dear vlad,
>
> Thank you for your help. My rmsd y-axis is in angstrom. I have run
> backbone atoms rmsd. Script is pasted below.
>
> trajin md_simulation_tac-comb.nc
> 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 Ali
> Junior 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.
>
>
> /Contact No://
> Office (92-21) 111222292 (Ext 309)//
> Email ID: saman.yousufali64.yahoo.com
> saman.ali.iccs.edu/
>
>
>
> On Friday, July 8, 2016 5:17 AM, Vlad Cojocaru
> <vlad.cojocaru.mpi-muenster.mpg.de> 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 ?
>
> Best
> Vlad
>
>
>
> 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<zmatovic.kg.ac.rs> <mailto:zmatovic.kg.ac.rs> wrote:
>>
>>
>> Hi,
>> 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.
>>
>> cheers
>> zoran
>>
>> 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]mpi-muenster.mpg.de
> http://www.mpi-muenster.mpg.de/43241/cojocaru
>
>
--
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]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/43241/cojocaru
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Received on Fri Jul 08 2016 - 06:00:06 PDT
