hard to say without details about the difference between this system and
the "relatively similar" one.
- you say it differs by a few amino acids. any different force field
libraries or parameters?
- did either have coordinates modeled in a different way? could those
different AA perhaps have some clash?
- did the minimization proceed similarly to the "good" system, with similar
energies (mdoutanalyzer.py)? anything different at the end of the
minimization?
On Fri, Sep 20, 2024 at 11:50 AM Maciej Spiegel via AMBER <amber.ambermd.org>
wrote:
> Hello AMBER Users,
>
> I am attempting to heat a system consisting of a solvated membrane bilayer
> with a protein. However, running this results in the following output
> https://pastebin.com/raw/hUY1DjAk — Etot is NaN and some things are
> ***********
> The system was initially minimized using the CPU (output:
> https://pastebin.com/raw/LEhMFnZ5 ) and then the GPU (output:
> https://pastebin.com/raw/LcQzadJY )
> Interestingly, a relatively similar system (only the protein differs by
> just a few amino acids) ran smoothly and is currently in the production
> phase.
>
> Could anyone suggest what the issue might be and how to resolve it?
> Thanks in advance!
>
> Thanks
> –
> Maciej Spiegel, MPharm PhD
> assistant professor
> .GitHub <https://farmaceut.github.io/>
>
> Department of Organic Chemistry and Pharmaceutical Technology,
> Faculty of Pharmacy, Wroclaw Medical University
> Borowska 211A, 50-556 Wroclaw, Poland
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Sep 20 2024 - 09:30:02 PDT
