In that case you probably need to track back through the various steps of
relaxation and determine when things started to go wrong. The
mdoutanalyzer tool can be helpful there, letting you plot the energy
components for each output file. when you determine when the energy started
to rise in 1 system vs the other, you might carefully visualize it to see
what happened. Usually the the time you see NaN or *** it's too late to
know the cause of the problem.
On Fri, Sep 20, 2024 at 12:18 PM Maciej Spiegel <maciej.spiegel.umw.edu.pl>
wrote:
> The systems were constructed in CHARMM-GUI using the same parameters: OPC
> water and ions, ff19SB, and the available lipid force field. (By the way,
> thanks for confirming that OPC is available there—I missed it, my mistake.)
>
> The coordinates are likely generated the same way since these are AF
> structures.
>
> I compared the outputs from both minimizations, and they are almost
> identical. There are no significant differences that suggest anything went
> wrong at these steps.
>
>
> Maciej Spiegel, MPharm PhD
> *assistant professor*
>
> *Department of Organic Chemistry **and **Pharmaceutical Technology,*
> *Faculty of Pharmacy, **Wroclaw Medical University*
> *Borowska 211A, **50-556 Wroclaw, Poland*
>
> Wiadomość napisana przez Carlos Simmerling <carlos.simmerling.gmail.com>
> w dniu 20 wrz 2024, o godz. 17:57:
>
>
> 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
>>
>
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Received on Fri Sep 20 2024 - 10:00:03 PDT
