Re: About changing charge/multiplicity during QM-MM

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon Mar 25 2019 - 09:33:55 CDT

Hi Kerlly
This has nothing to do with my question. A to your question, have a look at
previous posts under my name about this topic in this forum. You will find
all details. Notice that, in this case, orca is running in parallel on a
single node of 36 cores, letting namd occupy a single core only.
francesco

On Mon, Mar 25, 2019 at 8:47 AM McGuire, Kelly <mcg05004_at_byui.edu> wrote:

> 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
>

This archive was generated by hypermail 2.1.6 : Thu Dec 12 2019 - 23:20:36 CST