Re: vmd-l: ORCA Orbital Bug

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Mar 19 2019 - 12:39:43 CDT

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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