From: McGuire, Kelly (
Date: Wed Apr 10 2019 - 17:25:55 CDT

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


Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

From: John Stone <>
Sent: Wednesday, April 10, 2019 2:54 PM
To: McGuire, Kelly
Cc: VMD Mailing LIst
Subject: Re: vmd-l: File Format

  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--_000_BYAPR01MB4744D346D7A09135324F2AA0FF2E0BYAPR01MB4744prod_--