From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Mon Jun 11 2018 - 15:07:12 CDT

Wonderful, excited about that and the VR implementation in the future!

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 2:05:52 PM
To: McGuire, Kelly
Cc: VMD Mailing LIst
Subject: Re: vmd-l: VMD Update Questions

Hi,
  The existing 'orcaplugin' we have does read ORCA files, but I'm not
aware of and don't see any code therein that handles MOPAC logs,
so I expect that there's another (not yet finished?) MOPAC plugin
that they haven't sent me yet, or they are somehow translating
the output of MOPAC prior to invoking the existing ORCA plugin
on the output it produces. As I say, I'll have to ask my
colleagues and get back to you on this.

Best,
  John Stone

On Mon, Jun 11, 2018 at 07:48:55PM +0000, McGuire, Kelly 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<http://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

--
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/