VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jun 12 2018 - 15:54:48 CDT

Hi guys,
  So, I checked and indeed, the issue here is that our collaborators have had
a new MOPAC plugin in an early stage that has worked fine for their initial
usage, but they haven't yet sent a copy of it to me because their early
versions had a few limitations that they wanted to address first.
I'll let you know as soon as they send me a copy of the code and I can get it
incorporated into a VMD 1.9.4 test build.

Best,
  John

On Mon, Jun 11, 2018 at 04:11:52PM -0400, Axel Kohlmeyer wrote:
> 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;Â author: johns;Â 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 <[1]mcg05004_at_byui.edu>
> wrote:
>
> Thanks for looking into that! I found this on this webpage ->
> [2]http://www.ks.uiuc.edu/Research/qmmm/orbital.html:
>
> Loading orbitals from NAMD QM/MM calculations in
> VMD<[3]http://www.ks.uiuc.edu/Research/qmmm/orbital.html>
> [4]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 <[5]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,
> Â John Stone
> Â [6]vmd_at_ks.uiuc.edu
>
> On Mon, Jun 11, 2018 at 05:05:08PM +0000, McGuire, Kelly wrote:
> >Â Â Oh, I must have misunderstood the people at the QM/MM workshop.Â
> They said
> >Â Â that we would be able to
> >
> >Â Â visualize the QM/MM orbital results for both ORCA and MOPAC in
> 1.9.4
> >Â Â version...
> >
> >Â Â Kelly L. McGuire
> >
> >Â Â PhD Scholar
> >
> >Â Â Department of Physiology and Developmental Biology
> >
> >Â Â Brigham Young University
> >
> >Â Â LSB 3050
> >
> >Â Â Provo, UT 84602
> >
> >Â Â
> --------------------------------------------------------------------------
> >
> >Â Â From: John Stone <[7]johns_at_ks.uiuc.edu>
> >Â Â Sent: Monday, June 11, 2018 9:32:19 AM
> >Â Â To: McGuire, Kelly
> >Â Â Cc: VMD Mailing LIst
> >Â Â Subject: Re: vmd-l: VMD Update Questions
> >
> >Â Â Hi,
> >Â Â Â 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
> >Â Â inline with your questions below:
> >
> >Â Â On Tue, Jun 05, 2018 at 05:11:42PM +0000, McGuire, Kelly wrote:
> >Â Â >Â Â 1)Â The current VMD 1.9.4 Alpha can't load MOPAC orbitals
> from QM/MM
> >Â Â yet,
> >Â Â >Â Â is the next VMD update close to being available that will
> allow
> >Â Â >
> >Â Â >Â Â MOPAC orbital visualization?
> >
> >Â Â At the present time we don't have a plugin for reading MOPAC
> files
> >Â Â and to my knowledge I'm not aware of anyone that plans to
> contribute one
> >Â Â in the immediate short term, so I don't expect this to be
> available in the
> >Â Â VMD 1.9.4 release.
> >
> >Â Â >Â Â 2)Â I am about to purchase the HTC Vive Pro VR system and
> it made me
> >Â Â >Â Â wonder if VMD is going to be VR capable for
> >Â Â >Â Â this kind of system in the future, including using the
> Vive VR
> >  >  controllers? I am sure this would be a ways into the
> future,
> >Â Â >Â Â but just wondering if that is in the plans for VMD?
> >
> >  It is definitely in the plans... I've been in a holding pattern
> >Â Â waiting for the Khronos OpenXR standard v1.0 to be publically
> released
>
> --
> Dr. Axel Kohlmeyer  [8]akohlmey_at_gmail.com  [9]http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>
> References
>
> Visible links
> 1. mailto:mcg05004_at_byui.edu
> 2. http://www.ks.uiuc.edu/Research/qmmm/orbital.html
> 3. http://www.ks.uiuc.edu/Research/qmmm/orbital.html
> 4. http://www.ks.uiuc.edu/
> 5. mailto:johns_at_ks.uiuc.edu
> 6. mailto:vmd_at_ks.uiuc.edu
> 7. mailto:johns_at_ks.uiuc.edu
> 8. mailto:akohlmey_at_gmail.com
> 9. http://goo.gl/1wk0 

-- 
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/