I don't think Amber currently supports the combination of periodic box and
implicit solvent, but I'm surprised you don't get an error message about
it. Also, implicit solvent with explicit ions is a fairly new development,
see recent work by the Onufriev group for info. I think that tleap may
allow you to build this, but the resulting default parameters are not
likely to be very well optimized right now.
On Tue, Jul 30, 2024 at 12:30 PM Andriy Kovalenko via AMBER <
amber.ambermd.org> wrote:
> Hello,
>
> I am trying to run PMEMD minimization, heating, equilibration, and
> production stages for the SOD1 biomolecule with Na+ counterions in ambient
> water in a periodic box.
> However, Cedar terminates the run with an error message:
> - Program received signal SIGSEGV: Segmentation fault - invalid memory
> reference.
> Attached please see the output files and the input files (except for
> 3cqp_3_amb_period.parm7 which is of size 3,673K) for the heating run.
>
> My previous runs of this set but without a periodic box succeeded.
>
> Please advise how to resolve this issue with the periodic box runs.
>
> Sincerely,
>
>
> Dr. Andriy Kovalenko
>
> Researcher
> Department of Biological Sciences
> University of Alberta
> CW 405, Biological Sciences Bldg.
> Edmonton, Alberta, Canada T6G 2E9
>
> Tel: 780-940-7477 (cell)
> e-mail: andriy.kovalenko.ualberta.ca
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
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>
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Received on Tue Jul 30 2024 - 10:00:02 PDT
