Le 30/05/2026 à 17:36, Arti 2410204 via AMBER a écrit :
> ntp=3, csurften=3, gamma_ten=0.0, ninterface=2
>
> Unfortunately, I am still encountering the issue and have not yet been able
> to identify the underlying cause. I am continuing to investigate the system
> setup and simulation protocol to determine what might be contributing to
> the instability.
>
> Thank you again for your time and for the recommendation. I appreciate your
> help and will keep working on troubleshooting the problem.
Dear all,
Have you looked at the structures?
I have recently run into a problem where we had "old" cuda version
(11.x) and drivers (5xx),
and the system was blowing up, but a "simple" update of the software
stack solved the problem.
Otherwise, you can also use the exact protocl from JD. Callum (many
thanks for the github repo),
and see if the problem persists:
https://github.com/callumjd/AMBER-Membrane_protein_tutorial/tree/master/files_complete/MD_simulation
Using this protocol, every calculation runs fine for me.
HTH,
Stéphane
--
Maître de conférences Hors Classe, PEDR, HDR
US2B, Nantes Université, CNRS, UMR 6286, Team Structural Bioinformatics, F-44000 Nantes
http://www.us2b.univ-nantes.fr/ - http://www.steletch.org
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 04 2026 - 00:00:02 PDT
