Hi,
Carlos is right, what you're seeing (the instantaneous jumps) are
almost certainly imaging artifacts. The 'autoimage' command in cpptraj
is usually good at fixing these. E.g.
parm <topology>
trajin <trajectory>
autoimage
rms first <other keywords>
-Dan
On Fri, Dec 18, 2020 at 6:44 AM Vaibhav Dixit <vaibhavadixit.gmail.com> wrote:
>
> I calculated this in VMD (using RMSD trajectory tool) and used the option
> to Align.
> I'm not sure if it is equivalent to reimage in cpptraj.
> I will try with cpptraj and get back here in case the problem presists.
> thanks for suggesting.
>
> On Fri, Dec 18, 2020 at 4:58 PM Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > I agree that they are likely due to imaging, since they come back down
> > suddenly too.
> > did you try to reimage in cpptraj?
> >
> > On Fri, Dec 18, 2020 at 6:06 AM Vaibhav Dixit <vaibhavadixit.gmail.com>
> > wrote:
> >
> >> Dear All,
> >> I'm simulating a complex of two metalloproteins (120 ns trajectory).
> >> After about 80 ns, I'm observing a sudden jump in rmsd which looks
> >> unphysical but I'm not sure if it is due to some issue with wrapping.
> >> Visualization in VMD shows that one of the protein suddenly changes
> >> position.
> >> Both proteins seem to be well within the solvent box, thus I'm unable to
> >> guess what is the problem here.
> >> I have pasted two snapshots below in which the sudden jump is apparent.
> >> Please suggest to me ways in which I can check if these jumps are genuine
> >> or some type of artifact in the simulation.
> >> Thank you and best regards.
> >>
> >>
> >> [image: image.png]
> >>
> >> [image: image.png]
> >>
> >> [image: image.png]
> >>
> >> --
> >>
> >> Regards,
> >>
> >> Dr. Vaibhav A. Dixit,
> >>
> >> Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
> >> University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
> >> AND
> >> Assistant Professor,
> >> Department of Pharmacy,
> >> ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
> >> Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
> >> VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
> >> India.
> >> Phone No. +91 1596 255652, Mob. No. +91-7709129400,
> >> Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
> >> http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
> >> https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
> >>
> >> ORCID ID: https://orcid.org/0000-0003-4015-2941
> >>
> >> http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
> >>
> >> P Please consider the environment before printing this e-mail
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>
> --
>
> Regards,
>
> Dr. Vaibhav A. Dixit,
>
> Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
> University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
> AND
> Assistant Professor,
> Department of Pharmacy,
> ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
> Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
> VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
> India.
> Phone No. +91 1596 255652, Mob. No. +91-7709129400,
> Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
> http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
> https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
>
> ORCID ID: https://orcid.org/0000-0003-4015-2941
>
> http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
>
> P Please consider the environment before printing this e-mail
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Fri Dec 18 2020 - 06:30:03 PST
