VMD-L Mailing List

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Tue Mar 26 2019 - 10:15:25 CDT

  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 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

João

……………………………………………………...
João Vieira Ribeiro
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois

http://www.ks.uiuc.edu/~jribeiro/

jribeiro_at_illinois.edu<mailto: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