Fwd: About changing charge/multiplicity during QM-MM

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Apr 02 2019 - 09:36:47 CDT

As far as it matters, I have to correct my mail: actually the redox partner
carries negligible spin (0.5, against 3.9 for both iron ions), while,
unbound, it was a triplet. Previously I thought that 0.5 might be
significant, while probably not. At any event, all other atoms carry out
<0.00 spin, except one O-atom of iron-coordinated GLU, which carries 0.23
spin.
fp

---------- Forwarded message ---------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Sun, Mar 31, 2019 at 5:55 PM
Subject: Re: namd-l: About changing charge/multiplicity during QM-MM
To: Gerard Rowe <GerardR_at_usca.edu>

Hi Gerard
It was a problem with the cluster. By setting

--nodes=1
--ntasks=1
--cpus-per-task=1

the singlepoint had no problem.

I can read the Mulliken (or Loewdin) spin populations, so that I know where
the spin mostly resides (also the redox partner carries some spin), but I
am unable to get a plot of spin densities. With orca_plot I could generate
a cube file that is read by AVOGADRO but the output is limited to molecular
orbitals; apparently it does understand the alpha-beta difference.. With
VMD things went on even less satisfactorily. Any hint?
thanks
francesco

On Fri, Mar 29, 2019 at 5:09 PM Gerard Rowe <GerardR_at_usca.edu> wrote:

> If it still looks to a GBW for an initial guess, then you should be able
> to circumvent that by specifying an alternative initial guess method. Try
> adding PMODEL to your standard input line.
>
> ------------------------------
> *From:* Francesco Pietra <chiendarret_at_gmail.com>
> *Sent:* Thursday, March 28, 2019 12:49 PM
> *To:* Gerard Rowe
> *Cc:* namd-l_at_ks.uiuc.edu
> *Subject:* Re: namd-l: About changing charge/multiplicity during QM-MM
>
> Gerard
> Do you know how to set the keyword "noautostart" to orca. The keyword is
> mentioned in the instructions about restarting, however I was unable to get
> it accepted. For example "%scf noautostart end" failed. The point is that
> orca invents a gbw file even if none is present, and crashes because it
> does not find what was expected.
> thanks
> francesco
>
> On Tue, Mar 26, 2019 at 10:24 PM Gerard Rowe <GerardR_at_usca.edu> wrote:
>
> Unless your QM region is prohibitively large, it might be easier to just
> perform a single point calculation from scratch with the coordinates in the
> input file (i.e., remove the GBW file). That should avoid any issues.
>
> ------------------------------
> *From:* Francesco Pietra <chiendarret_at_gmail.com>
> *Sent:* Tuesday, March 26, 2019 4:55 PM
> *To:* Gerard Rowe
> *Subject:* Re: namd-l: About changing charge/multiplicity during QM-MM
>
> Gerard
> With full path to orca (4.1.1, the same path user for namd qmmm) same
> problem about the executable. In addition, a (for me) confusing allusion
> to basis sets.
> francesco
>
> WARNING!!!!!!!
> Your GBWFile is either corrupt or from a different ORCA version!
> Please be VERY careful with your calculation results!!!
>
> Data_size, sizeof( TOrcaInfo ): 497844, 491312
> ... Fine, the calculation information was read
> ... Fine, the file contains a basis set
> [file orca_tools/Tool-GTO-Bases/basissets.cpp, line 703]: TBasisList:
> Unable to read number of basis sets!
>
>
> On Tue, Mar 26, 2019 at 6:09 PM Gerard Rowe <GerardR_at_usca.edu> wrote:
>
> Hmm, it kind of looks like you either have a different number of atoms in
> your input than the program expects, or there are two different versions of
> orca installed on your system. You could try specifying the full path of
> Orca when running the program. That's the recommended way to do it for
> oMPI purposes, anyways.
>
> ------------------------------
> *From:* Francesco Pietra <chiendarret_at_gmail.com>
> *Sent:* Tuesday, March 26, 2019 12:35 PM
> *To:* Gerard Rowe
> *Cc:* NAMD
> *Subject:* Re: namd-l: About changing charge/multiplicity during QM-MM
>
> Hi Gerard:
> I copied the files that you indicated to a new folder. Then I modified
> qmmm_0.input by deleting "enGrad" from
> the first line of the .input file "! UKS BP86 RI SV def2/J enGrad KDIIS
> SOSCF"
> saving it as qmmm_0.noGrad.input, then launched a job
>
> srun orca qmmm_0.noGrad.input > qmmm_0.noGrad.log
>
> It crashed with message from .log file:
>
> Checking for AutoStart:
> The File: qmmm_0.noGrad.input.gbw exists (it was renamed by the system)
> Trying to determine its content:
>
> Checking for AutoStart:
> The File: qmmm_0.noGrad.input.gbw exists
> Trying to determine its content:
> ... Fine, the file contains calculation information
> ... Fine, the file contains calculation information
> ... Fine, the file contains calculation information
> ... Fine, the file contains calculation information
>
>
> WARNING!!!!!!!
> Your GBWFile is either corrupt or from a different ORCA version!
> Please be VERY careful with your calculation results!!!
>
> Data_size, sizeof( TOrcaInfo ): 744532, 491312
> ... Fine, the calculation information was read
> ... Fine, the file contains a basis set
>
> WARNING!!!!!!!
> Your GBWFile is either corrupt or from a different ORCA version!
> Please be VERY careful with your calculation results!!!
>
> Data_size, sizeof( TOrcaInfo ): 744532, 491312
> ... Fine, the calculation information was read
> ... Fine, the file contains a basis set
> [file orca_tools/Tool-GTO-Bases/basissets.cpp, line 706]: Wrong number of
> basis-sets stored!
>
> [file orca_tools/Tool-GTO-Bases/basissets.cpp, line 706]: Wrong number of
> basis-sets stored!
>
> [file orca_tools/Tool-GTO-Bases/basissets.cpp, line 706]: Wrong number of
> basis-sets stored!
>
> [file orca_tools/Tool-GTO-Bases/basissets.cpp, line 706]: Wrong number of
> basis-sets stored!
> ____
> The .err file said I/O operation failed.
> _________
>
> I don't understand that "Wrong number of basis set". The namd-qmmm
> simulation had been interrupted by the walltime.
> Could that be a reason for orca corrupted files?
>
> thanks
> francesco
>
>
>
> On Mon, Mar 25, 2019 at 7:34 PM Gerard Rowe <GerardR_at_usca.edu> wrote:
>
> Francesco,
>
> It sounds like you may have a fortunate outcome. I don't know the nature
> of your redox partner, but it's not an unreasonable assumption that the
> spin state will be the same between reactant and product if your partner
> becomes a ligand. If the redox partner started as a radical and became a
> closed-shell molecule, your final wavefunction is probably going to behave,
> and the trajectory could be well-suited for analysis through molecular
> orbital plots or spin-density plots. I think the most useful information
> will come out of spin density for a redox reaction. Things get more
> complicated (but not impossible) if the redox partner has unpaired
> electrons in it.
>
> As for carrying out stand-alone Orca calculations from the temp folder
> files of QM/MM, you should copy the inp, gbw, and point charge files into a
> new folder. Unless you have a lot of experience with QM programs, I'd
> stick to single point calculations here because you would have to play a
> tricky game of atomic restraints for QM geometry minimization.
>
> Your choice of level of theory is pretty good for QM/MM, but if I were
> trying to get a more reliable wavefunction, I'd probably change the basis
> set to def2-svp, and possibly specify def2-tzvp for the metal ion. If you
> don't have restrictions on how much CPU time you use for QM/MM, you may
> also play around with other local DFT functionals like PBE or M06L to see
> if they lead to different equilibrium structures. M06L, in particular, is
> parameterized to handle non-covalent interactions.
>
> -Gerard
>
>
>
>
> ------------------------------
> *From:* Francesco Pietra <chiendarret_at_gmail.com>
> *Sent:* Monday, March 25, 2019 12:09 PM
> *To:* NAMD; Gerard Rowe
> *Subject:* Re: namd-l: About changing charge/multiplicity during QM-MM
>
> Gerard:
> The redox partner is included but, regrettably, I have not yet carried out
> an analysis of what orca could tell. I simply observed that now the iron
> ions and the redox partner have reached a bonding distance, which remains
> stable on long QM-MM simulations, and the type of complex that is formed is
> experimentally known to have FeIII, never FeII. So, I came here much too
> early with my question, but, to go on, I'll take into account what you
> said. At any event the type of ligands of the Fe ions (in a protein) are
> for high spin, which over-complicates the matter. In addition, the
> simulation, because of the type and size of the system, was started at
> SlowConv but was continued at SOSCF in order to get convergence . All over
> it was at what might well be a too low level of DFT ("! UKS BP86 RI SV
> def2/J enGrad KDIIS SOSCF").
> Thanks
> francesco
>
> On Mon, Mar 25, 2019 at 3:53 PM Gerard Rowe <GerardR_at_usca.edu> wrote:
>
> Francesco,
>
> If your metal ion is definitely undergoing redox change, that's going to
> be very difficult to treat with QM/MM unless you have also included the
> redox partner in the QM region. Even then, it's going to be problematic
> because the spin state of your resulting system is unlikely to be
> reasonable. This is especially true if your final system is supposed to
> have unpaired electrons in different regions that aren't in communication
> anymore. What kind of system are you studying?
>
> I can imagine two scenarios where this will work out:
>
> 1. Your Fe(II) state is low-spin d6 (singlet) and the redox partner
> is a doublet. In the product state, The Fe(III) is a low-spin doublet and
> the redox partner is now a singlet.
> 2. Your Fe(II) state is high-spin d6 (sextet) and the redox partner is
> a singlet. In the product state, The Fe(III) is a high-spin quintet and
> the redox partner is now a doublet.
>
> If scenario 1 applies, you're in luck, and the spin system will be
> reasonable. If it's scenario 2, you're going to run into serious issues
> unless the redox partner happens to be bound to the metal. Long-range
> separation of unpaired spin in a DFT calculation often leads to problems
> and non-physical solutions. You can check the spin density of your
> resulting wavefunction in a similar way that you can visualize molecular
> orbitals.
>
> -Gerard
>
> ------------------------------
> *From:* owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of
> Francesco Pietra <chiendarret_at_gmail.com>
> *Sent:* Monday, March 25, 2019 3:16 AM
> *To:* NAMD
> *Subject:* namd-l: About changing charge/multiplicity during QM-MM
>
> I dare posing a general question on QM-MM, surely a naive question to
> those experienced with QM-MM (I am doing such simulations for the first
> time).
>
> I am observing a change in my metalloprotein system where apparently the
> iron ions become bounded to other ligands, changing from FeII to FeIII. The
> overall charge/multiplicity is not maintained, as far as I can understand.
> Nonetheless, ORCA is repeating its SCF cycles, converging after a number of
> cycles. I have already restarted the simulation six times for 24hr on 36
> cores with the same settings, in particular as to the charge and
> multiplicity, and the structure of the complex is no more changing, as far
> as it can be judged from geometry. I can't figure out how the system
> readjusts itself so that the QM calculation can go on.
> Thanks for any comment
> francesco pietra
>
>

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