VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 28 2019 - 22:44:13 CDT

Hi Kelly,
  Right now, the VMD GUIs for Orbital display are limited by the availability
of information that is provided by the underlying QM molfile plugins
that read the outpus of the quantum chemistry programs. The scripts that
Joao pointed out extend that in the specific case of the QM/MM codes that
have been made to work with NAMD, but they're not more broadly applicable
at present. It should be possible to create a GUI that addresses the issues
you're describing here, but VMD has to gauranteeably have the energies and
other information available at every timestep, and at least with several
of the QM molfile plugin parsers that presently exist, that is not yet
the case. This is something that I would very much like to improve as
time goes on, but it'll take some work on both the existing molfile parsers
and on the mofile plugin API for QM timestep data, and finally the GUI
itself.

Best,
  John

On Tue, Mar 26, 2019 at 03:15:25PM +0000, McGuire, Kelly wrote:
> Thanks Joao, I have actually been using that and it works great. What
> I'm asking for might be impossible or not worth the effort. Let's say I
> have a QM region that has about 100 atoms, and my results give hundreds of
> orbitals each frame. I'll have many HOMOs and many LUMOs e.g. HOMO,
> HOMO-1, HOMO-2, LUMO, LUMO+1, LUMO+2, etc. But, if I am only interested
> in orbitals around a certain atom, it could end up in any one of those
> depending on the orbital energy. For example, I am looking for a copper
> atom to bind to other atoms. Copper can have 6 bonds. Two of the bonds
> end up being HOMO for most of the frames. But, the other four are
> somewhere in HOMO-65 and HOMO-70, etc. One issue is that the orbital
> energies are changing each frame, so for one frame those two bonds are
> HOMO, in another frame they become HOMO-1 or HOMO-2, and then back to
> HOMO. So, is it possible to some how follow the bonding orbitals or any
> orbital of choice around a certain atom even if they are bouncing around
> HOMO, HOMO-1, etc.? I'm not sure what the selection criteria would be or
> if it's even possible.
>
> Kelly L. McGuire
>
> PhD Candidate
>
> Biophysics
>
> Department of Physiology and Developmental Biology
>
> Brigham Young University
>
> LSB 3050
>
> Provo, UT 84602
>
> --------------------------------------------------------------------------
>
> From: Joao Ribeiro <jribeiro_at_ks.uiuc.edu>
> Sent: Tuesday, March 26, 2019 7:16 AM
> To: McGuire, Kelly; vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: Visualization Question
>
>
> Hi Kelly,
>
>
>
> If I understood correctly, there is such an interface to do what you
> described at [1]https://www.ks.uiuc.edu/Research/qmmm/orbital.html. QwikMD
> also has something similar to this implemented to visualize and plot the
> orbitals (HOMO and LUMO) barriers over time.
>
>
>
> Best
>
>
>
> Joćo
>
>
>
>
>
> ...............................................................
> Joćo Vieira Ribeiro
> Theoretical and Computational Biophysics Group
> Beckman Institute, University of Illinois
>
> [2]http://www.ks.uiuc.edu/~jribeiro/
>
> [3]jribeiro_at_illinois.edu
>
> +1 (217) 3005851
>
>
>
> From: <owner-vmd-l_at_ks.uiuc.edu> on behalf of "McGuire, Kelly"
> <mcg05004_at_byui.edu>
> Date: Monday, March 25, 2019 at 7:06 PM
> To: "vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
> Subject: vmd-l: Visualization Question
>
>
>
> When an ORCA output file is opened in VMD through the orca viewer
> plugin, all of the orbitals are loaded. To keep this simple, let's say I
> do a purely QM geometry optimization on two molecules binding and not a
> QM/MM simulation. I open the output and I get all of the orbitals for
> both molecules in each of the geometry optimization steps. In this case,
> it took 100 steps to optimize, so I have 100 frames. I am not interested
> in all of the orbitals in both molecules, I'm just looking for one atom
> binding to a few of the atoms in other molecule. Now, HOMO and LUMO are
> usually the most interesting orbitals for reactions, but the atoms of
> interest aren't always part of the HOMO and LUMO in every frame.
> Sometimes they're higher up in the HOMO list or further down in the LUMO
> list. So, is it possible to follow the orbitals around certain atoms only
> and have those drawn, even though their energies might be bouncing around
> different HOMO and LUMO energy levels? It gets really difficult when
> there are 500 orbitals in the list and trying each frame to find the
> orbitals that are around certain atoms of interest, e.g. QM/MM simulations
> with hundreds to thousands of frames.
>
>
>
>
>
>
>
>
>
> Kelly L. McGuire
>
> PhD Candidate
>
> Biophysics
>
> Department of Physiology and Developmental Biology
>
> Brigham Young University
>
> LSB 3050
>
> Provo, UT 84602
>
>
>
> References
>
> Visible links
> 1. https://www.ks.uiuc.edu/Research/qmmm/orbital.html
> 2. http://www.ks.uiuc.edu/~jribeiro/
> 3. mailto:jribeiro_at_illinois.edu 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/