From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Sat Mar 16 2019 - 18:34:51 CDT
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
Department of Physiology and Developmental Biology
Brigham Young University
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
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?
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
> 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
> 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 http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349 http://www.ks.uiuc.edu/Research/vmd/
This archive was generated by hypermail 2.1.6 : Thu Dec 31 2020 - 23:17:10 CST