Re: vmd-l: ORCA Orbital Bug

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Tue Mar 19 2019 - 12:40:34 CDT

Correct, it is the a31 RTX build of VMD that now loads the orbitals correctly.

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: Tuesday, March 19, 2019 11:39 AM
To: McGuire, Kelly
Cc: VMD Mailing LIst; namd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: ORCA Orbital Bug

Kelly,
  Just so I know the details, you tested the new a31 RTX buid of VMD
on Linux, and that one worked fine for you? I'm at a conference this
week, so I'm not able to do much on this until I return home, but I wanted
to get the details correct in my notes, so I know where things stand when
I get back.

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Mar 19, 2019 at 05:31:43PM +0000, McGuire, Kelly wrote:
> John,
> I just installed the latest VMD, a31, and the orbital loading problem
> appears to have been fixed. In this version, I can now load all of my
> orbitals.
>
> 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: Sunday, March 17, 2019 6:19 PM
> To: McGuire, Kelly
> Cc: VMD Mailing LIst; namd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: ORCA Orbital Bug
>
> Kelly,
> Indeed, the mailing lists will silently block large file attachments
> from being posted, however I received what you sent since you included
> my email address in the To: line directly. I will have a look at this
> when I get back from the GPU conference in about a week. I'm sure you're
> right about the difference in behavior between the alpha12 and
> alpha27 versions of VMD, we're in the process of rewriting the code
> to make it more portable and we undoubtably broke something in the newer
> rev that now needs to be corrected.
>
> Best,
> John
>
> On Sat, Mar 16, 2019 at 11:34:51PM +0000, McGuire, Kelly wrote:
> > John,
> >
> > I responded to your email, but I attached a file. I'm not sure if
> > emails with attachments get through to the NAMD forum.
> >
> > 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: Saturday, March 16, 2019 12:13 AM
> > To: McGuire, Kelly
> > Cc: VMD Mailing LIst; namd-l_at_ks.uiuc.edu
> > Subject: Re: vmd-l: ORCA Orbital Bug
> >
> > Kelly,
> > This is undoubtably a limitation of the ORCA log parser.
> > Can you provide us with example files the demonstrate both the
> > working and non-working variants you've encountered?
> >
> > Best regards,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Fri, Mar 15, 2019 at 04:02:30PM +0000, McGuire, Kelly wrote:
> > > Not sure if this is an NAMD or VMD bug. In my QMMM NAMD config
> file
> > > (using ORCA), I have:
> > > qmConfigLine "!RI BP86 def2-SVP def2/J Grid5 NoFinalGrid EnGrad
> > NormalSCF
> > > printbasis"
> > > qmConfigLine "%%output PrintLevel Mini Print\[ P_Mulliken \] 1
> > > Print\[P_AtCharges_M\] 1 end"
> > > qmConfigLine "%%output Print\[ P_Basis \] 2 Print\[ P_MOs
> > > \] 1 end"
> > > qmConfigLine %%scf
> > > qmConfigLine maxiter 500
> > > qmConfigLine shift shift 0.1 erroff 0 end
> > > qmConfigLine damp fac 0.80 erroff 0.001 end
> > > qmConfigLine end
> > > I use grab_orcah.sh to concatenate the Orca outputs into a .orc
> file.
> > > When I try to open this in VMD and view the orbitals, VMD does
> not
> > load
> > > any orbitals. I also tried using orcaviewer.tcl to open the
> orca
> > viewer
> > > plugin, but no orbitals are loaded. This is what VMD's console
> > reads:
> > > orcaplugin) Orca version: 4.0.1
> > > Found commands.
> > > orcaplugin) No molecule charge found. Exiting
> > > orcaplugin) No molecule multiplicity found. Exiting
> > > orcaplugin) Number of electrons not found. Exiting
> > > New element found: H
> > > New element found: C
> > > New element found: N
> > > New element found: O
> > > New element found: Cu
> > > New element found: H
> > > orcaplugin) Parsed 975 uncontracted basis functions.
> > > orcaplugin) Filled basis arrays.
> > > orcaplugin) Found multiple appended gradient calculations: 12
> > > orcaplugin) Timestep 0:
> > > orcaplugin) ============
> > > orcaplugin) Number of SCF iterations: 36
> > > orcaplugin) Found wavefunction of type 0.
> > > orcaplugin) ERROR. Only s/p/d/f-shells are supported.
> > > orcaplugin) No canonical wavefunction present for timestep 0
> > > orcaplugin) Frames read: 1
> > > IF I remove the SCF block from my config file, then orbitals can
> be
> > > loaded. BUT, I need those SCF commands to help with
> convergence. If
> > I
> > > don't use it, my QMMM minimization takes 305 hours. With the
> SCF
> > block,
> > > it takes 90 hours.
> > >
> > > 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. [1]http://www.ks.uiuc.edu/~johns/
> > 2. [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
> [3]http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> [4]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/
> 3. http://www.ks.uiuc.edu/~johns/
> 4. 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/

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