From: daniele selli <daniele.selli.unimib.it>
Date: Thu, 18 Jan 2018 10:59:50 +0100

Dear Amber Users,

I am trying to use the QMMM implementation in AMBER with the DFTB
semiempirical method for the QM part.

When I run simple tests, like water dimer (one molecule DFTB and the other
one tip3p) optimization or a short MD simulation of a 15x15x15 ang water
box (3 molecules QM and 110 MM tip3p) I have no problem.
The code behaves well and I got reasonable results.

The problems come when I try to work with bigger systems!
I can still menage 5865 water molecules box, 113 of which are QM, but I
noticed that the code (sander.MPI) doesn't scale passing from 1 node (28
cores) to 2 nodes (56 cores) connect with infiniband of course.
Is there a reason for that? There is some special flag to enable during the
compilation or keyword to insert in the input of the qmmm calculation?

Then, if I have 6539 water molecules in total, 959 of which are QM the
calculation is essentially going nowhere. It is stacked and I cannot obtain
a single SCC cycle waiting a lot of time. This means that with the present
implementation of AMBER+SCC_DFTB one cannot handle systems with a QM region
so big or, again, I am missing something?
I have been using DFTB since a lot of time and ~1000 atoms is a normally
manageable size (using the DFTB+ code).

Thank you very much for you willingness and hopefully help,
Best Regards

Daniele Selli
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Received on Thu Jan 18 2018 - 02:30:02 PST
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