VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Apr 10 2019 - 17:23:25 CDT

It's in the VMD src distribution as:
  plugins/molfile_plugin/src/moldenplugin.c

You can also see the bleeding edge code (updated nightly) within
the VMD Doxygen docs here:
  https://www.ks.uiuc.edu/Research/vmd/plugins/doxygen/moldenplugin_8c-source.html

All of the molfile plugins are included there, in case you're curious
about the latest ORCA and other plugins too:
  https://www.ks.uiuc.edu/Research/vmd/plugins/doxygen/files.html

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Apr 10, 2019 at 09:41:34PM +0000, McGuire, Kelly wrote:
> What is the name of the source code file you looked at? Is it located in
> one of the VMD folders/
>
> Kelly L. McGuire
>
> PhD Candidate
>
> Biophysics
>
> Department of Physiology and Developmental Biology
>
> Brigham Young University
>
> LSB 3050
>
> Provo, UT 84602
>
> --------------------------------------------------------------------------
>
> From: John Stone <johns_at_ks.uiuc.edu>
> Sent: Wednesday, April 10, 2019 2:54 PM
> To: McGuire, Kelly
> Cc: VMD Mailing LIst
> Subject: Re: vmd-l: File Format
>
> Kelly,
> I didn't write the Molden plugin, but a quick read through the code
> indicates that it's determining the number of geometries/frames/timesteps
> to read from a particular Molden file section, and that it is NOT trying
> to read them in the form of concatenated output files. Apparently a
> single
> Molden output can contain multiple geometries/timesteps, so that's how
> the plugin was structured. It might be possible to teach VMD to allow
> you to use "mol addfile" to append a compatible QM config/run to an
> existing molecule in VMD, but a lot of work would have to go into checking
> that they use the same basis set and all of that, essentially all of the
> information that would normally be redundant among multiple output files
> that arise from the same input parameters.
>
> The Molden plugin was written long before the NAMD QM/MM feature
> (Molden orbital parsing was added 10 years ago), so this wasn't previously
> a consideration. We've been trying to get a Terachem license going
> here to be able to develop new support for it in the NAMD QM/MM feature,
> but that has been stalled waiting on the Stanford team for a technical
> issue with avoiding unnecessary Terachem restarts, as I understand it.
>
> In the mean time, you might read more of the Molden format and the
> moldenplugin source code, and you could probably modify it to
> allow the concatenation scheme you're using, or something like it.
> Until our QM/MM team have access to Terachem, there's probably
> not much we can do to help out with this particular issue in the
> short-term.
>
> Best regards,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Apr 10, 2019 at 08:15:17PM +0000, McGuire, Kelly wrote:
> > Anyone have any experience or ideas on how to read in .molden files
> that
> > have been concatenated during a QMMM, just as we can do with ORCA
> .out
> > files? I have concatenated my qmmm.molden files for each step, but
> when I
> > load it as a MOLDEN filetype, it just reads in the first output in
> the
> > concatenated file and ignores all of the other outputs. So far,
> using
> > Terachem instead of ORCA for my QMMM, I have ~4000 steps. I would
> like to
> > see the orbitals for each step just like with ORCA.
> >
> >
> > Kelly L. McGuire
> >
> > PhD Candidate
> >
> > Biophysics
> >
> > Department of Physiology and Developmental Biology
> >
> > Brigham Young University
> >
> > LSB 3050
> >
> > Provo, UT 84602
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> [1]http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> [2]http://www.ks.uiuc.edu/Research/vmd/
>
> References
>
> Visible links
> 1. http://www.ks.uiuc.edu/~johns/
> 2. http://www.ks.uiuc.edu/Research/vmd/ 

-- 
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/