VMD-L Mailing List

From: Marcelo C. R. Melo (melomcr_at_gmail.com)
Date: Fri Nov 04 2022 - 10:28:52 CDT

Hi Jing,
Yes, we can use VMD to render orbitals calculated with ORCA by saving
ORCA's output files.
Since ORCA's output files are huge, saving the orbital output at every step
of your QM/MM dynamics would take up GBs of space.
My suggestion (for practical purposes) is to select a few steps from your
simulation and use them to re-run NAMD with a single step of QM/MM energy
calculation (instead of doing "run 10000", just do "run 0"). Then
concatenate ORCA's outputs in a single text file so that VMD's plugin can
read all steps in sequence and create a video of the selected states along
your trajectory.

You can find an example for VMD's orbital rendering interface here:
http://www.ks.uiuc.edu/Research/qmmm/orbital.html

Best,
Marcelo

On Fri, Nov 4, 2022 at 10:17 AM jing liang <jingliang2015_at_gmail.com> wrote:

> Hi,
>
> on the website for QMMM simulations: http://www.ks.uiuc.edu/Research/qmmm/
> I can see some pictures of the MOs and I wonder if they were rendered with
> VMD?
> If that is the case does one need a special plugin? Thank you.
>