From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Jun 11 2018 - 15:11:52 CDT

this example is for ORCA, not MOPAC and the corresponding plugin was added
to the general VMD plugin source code rather recently (see the cvs log
below).

the alternate (and more traditional) approach to visualizing orbitals is to
let the QM software generate them and save them into a commonly understood
format, e.g. so-called .cube files, as they were popularized by the
gaussian QM software. VMD does support loading these kind of files with
gridded data, e.g. from .cube (and has been for a very long time).

axel.

RCS file: /vmd/cvsroot/plugins/molfile_plugin/src/orcaplugin.C,v
Working file: orcaplugin.C
head: 1.1
branch:
locks: strict
access list:
symbolic names:
keyword substitution: kv
total revisions: 1; selected revisions: 1
description:
----------------------------
revision 1.1
date: 2018/05/02 03:18:30; author: johns; state: Exp;
Added first rev of molfile plugin for reading ORCA files. Still needs to be
made more cross-platform portable and more broadly compilable with varying
C++ standards.
=============================================================================

On Mon, Jun 11, 2018 at 4:04 PM McGuire, Kelly <mcg05004_at_byui.edu> wrote:

> Thanks for looking into that! I found this on this webpage ->
> http://www.ks.uiuc.edu/Research/qmmm/orbital.html:
>
>
>
> Loading orbitals from NAMD QM/MM calculations in VMD<
> http://www.ks.uiuc.edu/Research/qmmm/orbital.html>
> www.ks.uiuc.edu
> Loading orbitals from NAMD QM/MM calculations in VMD. In quantum chemistry
> ab initio or DFT methods, molecular orbitals (MOs) are expressed in a
> discrete basis set expansion of Gaussian-type orbitals (GTOs).
>
>
>
> Loading orbitals from NAMD QM/MM calculations in VMD
>
> "In quantum chemistry ab initio or DFT methods, molecular orbitals (MOs)
> are expressed in a discrete basis set expansion of Gaussian-type orbitals
> (GTOs). The GTOs are given by the basis set definition, where multiple GTOs
> are contracted to a single GTO basis function.
>
> To extend the analysis capabilities for the QM/MM suite and its supported
> QM packages, we implemented a molfile plugin that is able to load the
> orbital information from both ORCA and MOPAC. The plugin is able to read a
> plethora of job types, such as single point calculations, geometry
> optimizations, and gradient calculations. Trajectories can be viewed by
> loading the appended output files for energy and gradient calculations
> performed by either ORCA or MOPAC during the QM/MM simulation without any
> workaround."
>
>
>
> Kelly L. McGuire
>
> PhD Scholar
>
> Department of Physiology and Developmental Biology
>
> Brigham Young University
>
> LSB 3050
>
> Provo, UT 84602
>
>
> ________________________________
> From: John Stone <johns_at_ks.uiuc.edu>
> Sent: Monday, June 11, 2018 1:08:48 PM
> To: McGuire, Kelly
> Cc: VMD Mailing LIst
> Subject: Re: vmd-l: VMD Update Questions
>
> I will double check on this with my colleagues, it is possible
> that one of the collaborators in Germany is working on a MOPAC plugin,
> but as I said, not that I'm personally aware of. I'll let you know
> what they say.
>
> Best,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Jun 11, 2018 at 05:05:08PM +0000, McGuire, Kelly wrote:
> > Oh, I must have misunderstood the people at the QM/MM workshop. They
> said
> > that we would be able to
> >
> > visualize the QM/MM orbital results for both ORCA and MOPAC in 1.9.4
> > version...
> >
> > Kelly L. McGuire
> >
> > PhD Scholar
> >
> > Department of Physiology and Developmental Biology
> >
> > Brigham Young University
> >
> > LSB 3050
> >
> > Provo, UT 84602
> >
> >
> --------------------------------------------------------------------------
> >
> > From: John Stone <johns_at_ks.uiuc.edu>
> > Sent: Monday, June 11, 2018 9:32:19 AM
> > To: McGuire, Kelly
> > Cc: VMD Mailing LIst
> > Subject: Re: vmd-l: VMD Update Questions
> >
> > Hi,
> > Sorry for the slow reply, I was travelling internationally with
> limited
> > access to wifi so I'm just catching up on emails now. See my answers
> > inline with your questions below:
> >
> > On Tue, Jun 05, 2018 at 05:11:42PM +0000, McGuire, Kelly wrote:
> > > 1) The current VMD 1.9.4 Alpha can't load MOPAC orbitals from
> QM/MM
> > yet,
> > > is the next VMD update close to being available that will allow
> > >
> > > MOPAC orbital visualization?
> >
> > At the present time we don't have a plugin for reading MOPAC files
> > and to my knowledge I'm not aware of anyone that plans to contribute
> one
> > in the immediate short term, so I don't expect this to be available
> in the
> > VMD 1.9.4 release.
> >
> > > 2) I am about to purchase the HTC Vive Pro VR system and it
> made me
> > > wonder if VMD is going to be VR capable for
> > > this kind of system in the future, including using the Vive VR
> > > controllers? I am sure this would be a ways into the future,
> > > but just wondering if that is in the plans for VMD?
> >
> > It is definitely in the plans... I've been in a holding pattern
> > waiting for the Khronos OpenXR standard v1.0 to be publically released

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.