Hi,
Vlad, your advice is quite justified. However, don't you think that in case
the solvent box is inappropriate the number of irregular frames would be
much larger? However, he should inspect trajectory and make sure that there
is no problem within modeled system.
Cheers
Zoran
-----Original Message-----
From: Vlad Cojocaru
Sent: Friday, July 8, 2016 4:29 PM
To: amber.ambermd.org
Subject: Re: [AMBER] rmsd plot error
It appears that you can skip that frame .. but take a look first in any
visualization program (VMD, Pymol, Chimera, whatever you are familiar
with) and make sure nothing else awkward is happening ...Sometimes,
hidden problems with your system may be revealed by this behavior ...
One problem that I know it can produce such issues is a box that is not
large enough to accommodate your molecule. Sometimes with the desire to
limit the number of solvent atoms in the system, the box size is chosen
at the limit and no checks on the periodic images are done during the
simulation.... There may be other problems as well .. Sure, it can
also be a simple corruption of that particular frame ...
I guess all I'm trying to say is: take decision only after you know what
exactly happens .....
Best
Vlad
On 07/08/2016 04:13 PM, zoran matovic wrote:
> Hi,
> As Vlad said the frame 20 is probably imaging related. Have u inspected
> (visualized) frame 20? I think that there is nothing wrong with your
> simulation, cpptraj commands and RMSD curve. If everything else is fine
> you
> can skip the frame 20 (warning says that is imaging problem).
>
> Cheers
> Zoran
>
> Dear Vlad,
> I have stripped affected frame. Now rmsd plot looks fine to me. I have
> attached it below. Some part of Rmsd file output is also pasted below. You
> can see that just frame 20 is affected. Can I skip this frame?
>
> #Frame RMSD_00000
> 1 0.0000
> 2 0.4813
> 3 0.5477
> 4 0.5479
> 5 0.5466
> 6 0.5554
> 7 0.5986
> 8 0.6139
> 9 0.6185
> 10 0.6465
> 11 0.7406
> 12 0.7192
> 13 0.7219
> 14 0.7102
> 15 0.7047
> 16 0.7385
> 17 0.7029
> 18 0.7287
> 19 0.6984
> 20 22.4429
> 21 0.6824
> 22 0.7099
> 23 0.7363
> 24 0.7176
> 25 0.7423
> 26 0.7416
> 27 0.7454
> 28 0.7704
> 29 0.7403
> 30 0.7612
> Best Regards, Sarah
>
> On Friday, July 8, 2016 5:47 AM, Vlad Cojocaru
> <vlad.cojocaru.mpi-muenster.mpg.de> wrote:
>
>
> 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>
> 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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>
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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
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Received on Fri Jul 08 2016 - 08:00:03 PDT
