VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Mar 19 2019 - 13:04:58 CDT
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There are lots of ways that could potentially occur.
Collect the cases that cause problems, and we'll figure it
out when I'm back home from travel.
Best,
John Stone
vmd_at_ks.uiuc.edu
On Tue, Mar 19, 2019 at 05:43:30PM +0000, McGuire, Kelly wrote:
> Wait, I just tried to open a different QMMM simulation, and this time the
> a31 RTX build did NOT load the orbitals and I am getting the same error
> again. Not sure how it could work for one and not the other.
>
> 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. [1]http://www.ks.uiuc.edu/~johns/
> > 2. [2]http://www.ks.uiuc.edu/Research/vmd/
> > 3. [3]http://www.ks.uiuc.edu/~johns/
> > 4. [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
> [5]http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> [6]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/
> 5. http://www.ks.uiuc.edu/~johns/
> 6. 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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- In reply to: McGuire, Kelly: "Re: ORCA Orbital Bug"
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