Is the initial structure reliable?
On Sat, Nov 9, 2024, 6:40 AM Maciej Spiegel <maciej.spiegel.umw.edu.pl>
wrote:
> Not at all: Ol21+OL3+OPC water/ions, with missing parameters taken from
> GAFF2 (vide frcmod files, annotated as such )
>
>
> Maciej Spiegel, MPharm PhD
> *assistant professor*
>
> *Department of Organic Chemistry **and **Pharmaceutical Technology,*
> *Faculty of Pharmacy, **Wroclaw Medical University*
> *Borowska 211A,
> <https://www.google.com/maps/search/Borowska+211A,+50-556+Wroclaw,+Poland?entry=gmail&source=g> **50-556
> Wroclaw, Poland
> <https://www.google.com/maps/search/Borowska+211A,+50-556+Wroclaw,+Poland?entry=gmail&source=g>*
>
> Wiadomość napisana przez Carlos Simmerling <
> carlos.simmerling.stonybrook.edu> w dniu 9 lis 2024, o godz. 12:32:
>
>
> Perhaps you mentioned this earlier in the thread, but are you using any
> custom or non-standard force field libraries? In my experience this is
> often the issue when other things seem standard.
>
> On Sat, Nov 9, 2024, 4:14 AM Maciej Spiegel via AMBER <amber.ambermd.org>
> wrote:
>
>> The hydrogen mass-repartitioned topology was created using CPPTraj (
>> https://amberhub.chpc.utah.edu/creating-a-repartitioned-topology/ ). I
>> verified the mass modifications with the same software, and the values are
>> adjusted as expected.
>>
>> Following the protocol described in 10.1063/5.0013849 <
>> https://doi.org/10.1063/5.0013849> yesterday, the periodic box error was
>> resolved. However, a new error occurred: "Error: an illegal memory access
>> was encountered launching kernel kNLSkinTest
>> Error: an illegal memory access was encountered launching kernel
>> kNLSkinTest” This error led to some production runs failing (no footer in
>> the output file and truncated frames), not at the beginning but towards the
>> final nanoseconds of the Nth run.
>>
>> Monte Carlo sampling is already being applied.
>> Attaching all relevant files: https://we.tl/t-pBxfxcLaf2
>> By the way, ‚checkstructure’ of CPPTraj does not indicate errors other
>> than "Warning: Atoms 34826:WAT_8505.H1 and 34828:WAT_8505.EPW are close
>> (0.78)” but I use OPC water so not relevant, I suppose.
>>
>> 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
>> <https://www.google.com/maps/search/Borowska+211A,+50-556+Wroclaw,+Poland?entry=gmail&source=g>
>>
>> > Wiadomość napisana przez David A Case <dacase1.gmail.com> w dniu 9 lis
>> 2024, o godz. 00:55:
>> >
>> > On Fri, Nov 08, 2024, Maciej Spiegel via AMBER wrote:
>> >
>> >> Encountered error: „ERROR: Calculation halted. Periodic box dimensions
>> >> have changed too much from their initial values.
>> >> Your system density has likely changed by a large amount, probably from
>> >> starting the simulation from a structure a long way from equilibrium."
>> >>
>> >> I run my simulations in 10 x 10 ns jobs using GPU. They keep failing at
>> >> various stages, not just at the first interval—one job even terminated
>> >> in the 9th interval! Although the errors suggest this might be due to
>> >> significant density fluctuations, the density remains within the range
>> of
>> >> 1.0355 to 1.0383. I inspected the MD trajectory and didn’t notice any
>> >> specific issues.
>> >
>> >> I use H-mass repartitioned topology generated with CPPTRAJ.
>> >
>> > It might help to know exactly how you applied H-mass repartitioning.
>> Have
>> > you checked the masses in the prmtop file (with an editor, or with
>> parmed)
>> > to make sure they are OK?
>> >
>> > A second idea, longshot: try some runs with NVT rather than NPT: does
>> the
>> > problem go away? If it does, try NPT but with barostat=2.
>> >
>> > But overall, it looks like something is triggering a failure, and doing
>> > enough damage to lead to an incorrect error message. Others on the
>> list may
>> > see something that rings a bell. But we may need to get enough files
>> to try
>> > to reproduce the problem.
>> >
>> > ...good luck...dac
>> >
>>
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Received on Sat Nov 09 2024 - 04:00:02 PST
