VMD-L Mailing List

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Mon Mar 25 2019 - 19:05:45 CDT

     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