VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Mar 19 2019 - 13:04:58 CDT

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/