Re: About changing charge/multiplicity during QM-MM

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Mon Mar 25 2019 - 02:47:14 CDT

  Sorry, I'm not sure about your question. But, I am curious. How did you get ORCA to run in parallel with NAMD on 36 cores? Mine runs, but the ORCA .TmpOut file stops at Pre-Screening Matrix. The simulation keeps running, but the output does not move forward and it doesn't look like the simulation is actually running. I don't get any errors or indication that something is wrong. Where do you have your files set up? What does your submit script look like?

Kelly L. McGuire

PhD Candidate

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

________________________________
From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of Francesco Pietra <chiendarret_at_gmail.com>
Sent: Monday, March 25, 2019 1:16 AM
To: NAMD
Subject: namd-l: About changing charge/multiplicity during QM-MM

I dare posing a general question on QM-MM, surely a naive question to those experienced with QM-MM (I am doing such simulations for the first time).

I am observing a change in my metalloprotein system where apparently the iron ions become bounded to other ligands, changing from FeII to FeIII. The overall charge/multiplicity is not maintained, as far as I can understand. Nonetheless, ORCA is repeating its SCF cycles, converging after a number of cycles. I have already restarted the simulation six times for 24hr on 36 cores with the same settings, in particular as to the charge and multiplicity, and the structure of the complex is no more changing, as far as it can be judged from geometry. I can't figure out how the system readjusts itself so that the QM calculation can go on.
Thanks for any comment
francesco pietra

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