VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Apr 10 2019 - 17:30:55 CDT

The issue with orbital energies is expected. We'll have to see if
we can add parsing of that info to the Molden plugin. If you're getting
empty outputs for those, that's just because it isn't reading them in.

Best,
  John

On Wed, Apr 10, 2019 at 10:25:55PM +0000, McGuire, Kelly wrote:
> Hey John, I think I found a quick work around for now. If you save the
> .molden files every step with a different name, e.g. qmmm1.molden,
> qmmm2.molden, etc, for each step, then open the first file in VMD, and
> then load the other files onto the loaded file, it will open the
> additional files as separate frames and you can play it like a trajectory
> just like we do with ORCA. Of course, you will end up with the same
> number of files as steps, but the total size is the same as if they were
> concatenated into one file. I tested this with the first 5 steps. I just
> need to get my QMMM config file to save the qmmm.molden files with
> different names each step somehow.
> One other thing I have noticed, might be a bug, is that when I use the TK
> console to get orbital energies, it just prints out empty brackets.
> molinfo top get orbenergies, molinfo top get orboccupancies, and the other
> commands don't work with the molden files, at least not in 1.9.4a12.
>
> 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/