Dear Amber Developers,
I am currently performing QM/MM molecular dynamics simulations using sander.MPI, and I have some questions regarding the parallelization strategy of the QM part.
>From the output of my simulation, I see messages such as:
"QMMM: Quantum atom + link atom division among threads"
where the QM region (including link atoms) is divided among multiple threads (e.g., 32 threads). Each thread is assigned a subset of QM atoms.
For classical molecular dynamics simulations, it is straightforward to understand: each thread is responsible for computing the potential energy and forces of all atoms within its assigned spatial region, and the results from all threads are then combined. However, for QM/MM molecular dynamics, due to the special nature of the QM region calculations, it is not possible to treat atoms in different regions independently as in classical MD. In this case, how does sander.MPI actually work?
Thank you very much for your time and assistance. I truly appreciate your help and any insights you can provide regarding my question.
I look forward to your response.
Best regards,
Weihao Zhang
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Apr 29 2026 - 02:00:03 PDT
