Small correction: The DFTB+ interface is not fully functional and is not scheduled for release yet.
All the best,
Andy
—
Dr. Andreas W. Goetz
Assistant Research Scientist
San Diego Supercomputer Center
Tel: +1-858-822-4771
Email: agoetz.sdsc.edu
Web: www.awgoetz.de
> On Jan 18, 2018, at 5:22 AM, Gustavo Seabra <gustavo.seabra.gmail.com> wrote:
>
> Unfortunately, this is the expected behavior for the DFTB code in sander.
> The code runs all in processor, and is not parallel. This has to do with
> the diagonalization routines, that are not parallel.
>
> If you are used to DFTB+, maybe you could try the new interface that uses
> it as an external QM code.
>
> --
> Gustavo Seabra
>
> Em 18 de jan de 2018 07:00, "daniele selli" <daniele.selli.unimib.it>
> escreveu:
>
>> 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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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Thu Jan 18 2018 - 11:30:03 PST
