Display comprehensive MO of QM part of QM-MM

To give a better idea of what happens, please have a look to the attached
screenshot for homo.The wavefunction is for the whole system, not for the
part highlighted with mos
francesco

On Sat, May 30, 2020 at 6:26 PM Francesco Pietra chiendarret@users.sourceforge.net wrote:

I forgot showing the terminal output

reading isosurface data from /home/francesco/tmp/qmmm_0.input.mo495a.cube
isosurface1 created with cutoff=0.02 min=-0.20028901 max=0.155882;
isosurface count:1
isosurface full data range -1.0 to 1.0 with color scheme spanning -1.0 to
1.0

On Sat, May 30, 2020 at 5:20 PM Francesco Pietra
chiendarret@users.sourceforge.net %0Dchiendarret@users.sourceforge.net
wrote:

---

• [patches:#37] https://sourceforge.net/p/jmol/patches/37/
  https://sourceforge.net/p/jmol/patches/37/ Display
  comprehensive MO of QM part of QM-MM*

Status: open
Group: v1
Created: Sat May 30, 2020 03:20 PM UTC by Francesco Pietra
Last Updated: Sat May 30, 2020 03:20 PM UTC
Owner: nobody

With the ORCA-generated cube file for HOMO of the QM part of a NAMD-ORCA
QM-MM simulation,
commands

$ load xyz file
$isosurface sign homo-cube file

shows MO for only one of the seven molecules that compose the QM part of
the QM-MM simulation. I have tried various combinations of commands without
being able to visualize the MO for the system. I also suspect that the MO
shown as above for one of the molecules has no physical signicance.
The same for LUMO, which shows MO for a different component molecule.

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https://sourceforge.net/p/jmol/patches/37/

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---

• [patches:#37] https://sourceforge.net/p/jmol/patches/37/ Display
  comprehensive MO of QM part of QM-MM*

Status: open
Group: v1
Created: Sat May 30, 2020 03:20 PM UTC by Francesco Pietra
Last Updated: Sat May 30, 2020 03:20 PM UTC
Owner: nobody

With the ORCA-generated cube file for HOMO of the QM part of a NAMD-ORCA
QM-MM simulation,
commands

$ load xyz file
$isosurface sign homo-cube file

shows MO for only one of the seven molecules that compose the QM part of
the QM-MM simulation. I have tried various combinations of commands without
being able to visualize the MO for the system. I also suspect that the MO
shown as above for one of the molecules has no physical signicance.

The same for LUMO, which shows MO for a different component molecule.

Sent from sourceforge.net because you indicated interest in
https://sourceforge.net/p/jmol/patches/37/

To unsubscribe from further messages, please visit
https://sourceforge.net/auth/subscriptions/