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-- 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 > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Thu Jan 18 2018 - 05:30:03 PST