Re: QM/MM Question

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Tue Nov 06 2018 - 13:40:14 CST

  I found a post by Marcelo that says ENGRAD is always required in the qmConfigLine. I added that, and now there is a convergence issue. I set the tolerance to NormalSCF, and my system does reach 10e-6 within 60 cycles, but the scf calculations keep going and it says convergence not reached after 125 cycles, and below that the tolerance shows set to 10e-8. I think my path variables are set up correctly and this would work if I can get the tolerance set to 10e-6 instead of 10e-8...Here is my NAMD config input for ORCA:

qmConfigLine "! RI BP86 SVP"
qmConfigLine "! UKS NormalSCF slowConv"
qmConfigLine "! Grid4 ENGRAD printbasis"

  Is NormalSCF being overwritten somehow or is this format incorrect?

Kelly L. McGuire

PhD Scholar

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

________________________________
From: Gerard Rowe <GerardR_at_usca.edu>
Sent: Tuesday, November 6, 2018 12:17:42 PM
To: McGuire, Kelly; namd-l_at_ks.uiuc.edu
Subject: Re: QM/MM Question

That looks like an issue with how your parallel environment is set up. Are you possibly using environment variables when designating the path to your working directory? Or is the QM calculation running on a different node? I'm not familiar with SLURM, so I can't really give specific advice here.

________________________________
From: McGuire, Kelly <mcg05004_at_byui.edu>
Sent: Monday, November 5, 2018 10:23:11 PM
To: Gerard Rowe; namd-l_at_ks.uiuc.edu
Subject: Re: QM/MM Question

Ok, I got my SCF calculation to converge in 88 cycles. However, after the first SCF calculation is done, my QM/MM minimization stops. I have my .config set to run 100 steps of minimization, but it stops. Am I missing a command to continue after the first SCF calculation? The errors are:

1) NAMD LOG File:

TCL: Minimizing for 100 steps
Info: List of ranks running QM simulations: 0.
ERROR: Could not find QM output file!
FATAL ERROR: (unknown error): No such file or directory

The path to my QM/MM output have permissions granted...what output is it looking for?

2) SLURM FILE:

Reason: FATAL ERROR: (unknown error): No such file or directory

Charm++ fatal error:
FATAL ERROR: (unknown error): No such file or directory

3) ORCA .TmpOut File (No Errors):

                            ***************************************
                            * ORCA property calculations *
                            ***************************************

                                    ---------------------
                                    Active property flags
                                    ---------------------
   (+) Dipole Moment

------------------------------------------------------------------------------
                       ORCA ELECTRIC PROPERTIES CALCULATION
------------------------------------------------------------------------------

Dipole Moment Calculation ... on
Quadrupole Moment Calculation ... off
Polarizability Calculation ... off
GBWName ... /panfs/pan.fsl.byu.edu/scr/grp/busathlab/kmcguir2/m2drugsimulations/NAMD/Tutorials/QwikMD/InfluenzaAM2/Drugs/S31N/Cu/FreeCu/Simulations/QMMM/ORCA/Simulation/run/qmmm_exec/QMMM-Min/0/qmmm_0.input.gbw
Electron density file ... /panfs/pan.fsl.byu.edu/scr/grp/busathlab/kmcguir2/m2drugsimulations/NAMD/Tutorials/QwikMD/InfluenzaAM2/Drugs/S31N/Cu/FreeCu/Simulations/QMMM/ORCA/Simulation/run/qmmm_exec/QMMM-Min/0/qmmm_0.input.scfp.tmp
The origin for moment calculation is the CENTER OF MASS = (-0.398250, -0.891828 -9.600489)

-------------
DIPOLE MOMENT
-------------
                                X Y Z
Electronic contribution: 0.82027 -24.74688 -6.06960
Nuclear contribution : 0.17820 22.50277 -0.13996
                        -----------------------------------------
Total Dipole Moment : 0.99847 -2.24410 -6.20956
                        -----------------------------------------
Magnitude (a.u.) : 6.67769
Magnitude (Debye) : 16.97335

Timings for individual modules:

Sum of individual times ... 3417.899 sec (= 56.965 min)
GTO integral calculation ... 3.915 sec (= 0.065 min) 0.1 %
SCF iterations ... 3413.984 sec (= 56.900 min) 99.9 %
                             ****ORCA TERMINATED NORMALLY****
TOTAL RUN TIME: 0 days 0 hours 57 minutes 7 seconds 185 msec

Kelly L. McGuire

PhD Scholar

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

________________________________
From: Gerard Rowe <GerardR_at_usca.edu>
Sent: Monday, November 5, 2018 3:19:08 PM
To: McGuire, Kelly; namd-l_at_ks.uiuc.edu
Subject: Re: QM/MM Question

Unless you have a huge number of atoms, going over 250 iterations isn't useful. If that doesn't work, you may have to walk a long road of trying different convergence aids to achieve a good wavefunction.

________________________________
From: McGuire, Kelly <mcg05004_at_byui.edu>
Sent: Monday, November 5, 2018 2:46:39 PM
To: Gerard Rowe; namd-l_at_ks.uiuc.edu
Subject: Re: QM/MM Question

Excellent, that worked, thanks! In your opinion, what is the maxIter you would try before looking at starting geometry problems or changing things like basis set, level of theory, etc..?

Kelly L. McGuire

PhD Scholar

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

________________________________
From: Gerard Rowe <GerardR_at_usca.edu>
Sent: Monday, November 5, 2018 12:41:11 PM
To: McGuire, Kelly; namd-l_at_ks.uiuc.edu
Subject: Re: QM/MM Question

That should definitely work. Make sure you use something like: qmConfigLine "%%scf maxiter 500 end"

The two percent signs are necessary for the input file to be constructed properly.

________________________________
From: McGuire, Kelly <mcg05004_at_byui.edu>
Sent: Monday, November 5, 2018 1:14:02 PM
To: Gerard Rowe; namd-l_at_ks.uiuc.edu
Subject: Re: QM/MM Question

  My calculations won't converge after 125 iterations. I tried increasing the iterations:

%scf

MaxIter 500

end

    But it says that MaxIter is unrecognized...I followed the manual...is there a different way to increase max iterations for version 4.0.1?

Kelly L. McGuire

PhD Scholar

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

________________________________
From: Gerard Rowe <GerardR_at_usca.edu>
Sent: Monday, November 5, 2018 6:32:06 AM
To: namd-l_at_ks.uiuc.edu; McGuire, Kelly
Subject: Re: QM/MM Question

I don't think Orca has somehting like that. Gaussian has a feature they call ONIOM that can achieve what you describe. However, for bonded atoms that are the focus of the calculation, it's not a good idea to use different levels of theory because the boundary atoms won't behave correctly. Orca does have some computational shortcuts you can use to speed up the calculation, though. If you use a pure DFT functional like BP86 or M06L, you can take advantage of the RI approximation for a massive speedup with little loss in accuracy. You also want to use as small of a basis set as possible, which is probably going to be "sv" or "def2-svp".

See this page for a quick tutorial.

https://sites.google.com/site/orcainputlibrary/dft6771286681672674&sdata=cU143Z62wVFINmyYjt2EA72DYkB291mcPtgN3z70znY%3D&reserved=0>

The Orca manual is much more extensive and explains the keywords better.

-Gerard

________________________________
From:
owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of McGuire, Kelly <mcg05004_at_byui.edu>
Sent: Sunday, November 4, 2018 1:59:51 PM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: QM/MM Question

  A bit of an ignorant question, but does anyone know if it's possible with the NAMD QM/MM to use different theories with different atoms in the QM region? I ask because I have a divalent copper ion, 12 water molecules, and four histidine sidechains in my QM region. MP2 or HF is taking a very long time to complete just one step. ORCA doesn't have PM7. I am using MOPAC's PM7, but I'm not sure when we'll be able to open mopac output files in VMD to view the orbitals. So, with ORCA QM/MM, can I maybe use PM3 for the waters and histidines, and assign copper with MP2 or HF in the same run? Or would that be bad to use different levels of theory in the same region? Thanks!

Kelly L. McGuire

PhD Scholar

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

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