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
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http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Dec 18 2020 - 04:00:02 PST
