From: Marcelo C. R. Melo (melomcr_at_gmail.com)
Date: Thu Sep 09 2021 - 12:09:00 CDT
Hi Herald,
I may have a couple of suggestions and questions for you.
1. Is 75.000 the total number of atoms in your entire system, or in your QM
regions? How large is the QM region itself?
If you have more than a few hundred atoms in your QM region, I would expect
ORCA to take a while to calculate it.
2. In your NAMD execution line, you could ask for fewer nodes, like 5 or
10, and leave the rest for ORCA.
For example:
NAMD2 -> namd2 +p10 Min.conf
ORCA -> qmConfigLine "% PAL NPROCS 30 END" (from Min.conf)
3. If you only have one QM region in your system, you only need to ask for
1 QM simulations per node. This won't change your calculation.
4. What kind of QM calculation are you running? semi empirical? HF?
Best,
Marcelo
On Thu, 9 Sept 2021 at 06:53, Herald Delis <bioinfo2021great_at_gmail.com>
wrote:
> [image: image.gif]Dear All,
>
> I am trying to run QMMM-MD using orca-namd2.
> But it happens to be too slow, I wanted to know if I am doing something
> wrong or is there a better way.
> I have a CPU node with 40 cores (and 4 unused GPU), my calculations of
> 75,000 atoms QMMM-Minimization takes 4 days.
>
> NAMD2 -> namd2 +p22 Min.conf
> ORCA -> qmConfigLine "% PAL NPROCS 20 END" (from Min.conf)
>
> # Number of simultaneous QM simulations per node
> QMSimsPerNode 20
>
> Thanks and regards,
> Herald
>
>
>
>
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