From: Marcelo C. R. Melo (melomcr_at_gmail.com)
Date: Tue Jan 17 2017 - 15:58:58 CST
Sure, you could minimize, equilibrate (with and/or without constraints) and
run you system for some time before selecting a conformation to be used in
the TCL script, and then initiating QM/MM runs. There is nothing in the
method or code that would prevent you from doing that.
Some discussion could ensue regarding the difference in force fields used
for minimizing/equilibrating and then running the simulations, so you
should check the literature for your particular case for that.
Best,
Marcelo
--- Marcelo Cardoso dos Reis Melo PhD Candidate Luthey-Schulten Group University of Illinois at Urbana-Champaign crdsdsr2_at_illinois.edu +1 (217) 244-5983 On 17 January 2017 at 12:10, Francesco Pietra <chiendarret_at_gmail.com> wrote: > Hi Marcelo: > > Adding "ENGRAD" let the simulation running. It was running on 6 cores, > therefore much too slow for this system. Killed while minimization was > slowly moving atoms. > > Probably obvious; can minimization be run separately, submitting to > "prepare.qm.region.tlc" minimized (perhaps also "heated") files? > > Nonetheless I would be happy to have the simulation running with MOPAC > too; with DFT, especially with BP86, one does not not where he is as to the > spin state. > > Thanks a lot > > francesco pietra > > On Mon, Jan 16, 2017 at 11:17 PM, Marcelo C. R. Melo <melomcr_at_gmail.com> > wrote: > >> In the case of ORCA, you should always have the keyword "ENGRAD" in your >> qmConfigLine. This tells ORCA to write a file ending in "engrad" where the >> gradient is written. >> >> That should solve your issue. >> >> Marcelo >> >> --- >> Marcelo Cardoso dos Reis Melo >> PhD Candidate >> Luthey-Schulten Group >> University of Illinois at Urbana-Champaign >> crdsdsr2_at_illinois.edu >> +1 (217) 244-5983 <(217)%20244-5983> >> >> On 16 January 2017 at 01:55, Francesco Pietra <chiendarret_at_gmail.com> >> wrote: >> >>> Hello: >>> >>> This mail in parallel to previous mail about the same system and same >>> issue with QM-MM MOPAC. >>> >>> System of total spin 7 (total six unpaired electrons on two open shell >>> molecules) >>> >>> qmConfigLine "! UKS BP86 def2-TZVP def2-TZVP/J KDIIS SOSCF" >>> qmConfigLine "%%output PrintLevel Mini Print\[ P_Mulliken \] 1 >>> Print\[P_AtCharges_M\] 1 end" >>> # Multiplicity of the QM region. This is needed for propper >>> # construction of ORCA's input file. >>> qmMult "1 7" >>> The gmConfigLine is the best for transition metals in my experience with >>> orca) >>> >>> Folder /0 contains >>> qmmm_0.input >>> qmmm_0.input.gbw >>> qmmm_0.input.pntchrg >>> qmmm_0.input.prop >>> qmmm_0.input.TmpOut >>> >>> The TmpOut file: >>> >>> Total SCF time: 0 days 1 hours 14 min 18 sec >>> >>> ------------------------- -------------------- >>> FINAL SINGLE POINT ENERGY nan >>> ------------------------- -------------------- >>> >>> >>> *************************************** >>> * ORCA property calculations * >>> *************************************** >>> >>> --------------------- >>> Active property flags >>> --------------------- >>> (+) Dipole Moment >>> >>> >>> ------------------------------------------------------------ >>> ------------------ >>> ORCA ELECTRIC PROPERTIES CALCULATION >>> ------------------------------------------------------------ >>> ------------------ >>> >>> Dipole Moment Calculation ... on >>> Quadrupole Moment Calculation ... off >>> Polarizability Calculation ... off >>> GBWName ... >>> /dev/shm/NAMD_4IEV/0/qmmm_0.input.gbw >>> Electron density file ... /dev/shm/NAMD_4IEV/0/ >>> qmmm_0.input.scfp.tmp >>> >>> ------------- >>> DIPOLE MOMENT >>> ------------- >>> X Y Z >>> Electronic contribution: 4.59465 27.21307 -7.80847 >>> Nuclear contribution : -16.01483 -32.18596 12.99059 >>> ----------------------------------------- >>> Total Dipole Moment : -11.42018 -4.97289 5.18211 >>> ----------------------------------------- >>> Magnitude (a.u.) : 13.49090 >>> Magnitude (Debye) : 34.29115 >>> >>> >>> Timings for individual modules: >>> >>> Sum of individual times ... 4508.572 sec (= 75.143 min) >>> GTO integral calculation ... 8.134 sec (= 0.136 min) >>> 0.2 % >>> SCF iterations ... 4500.439 sec (= 75.007 min) >>> 99.8 % >>> ****ORCA TERMINATED NORMALLY**** >>> TOTAL RUN TIME: 0 days 1 hours 15 minutes 27 seconds 331 msec >>> >>> >>> The NAMD log: >>> >>> TCL: Minimizing for 100 steps >>> Info: List of ranks running QM simulations: 0. >>> ERROR: Could not find QM output file! >>> FATAL ERROR: No such file or directory >>> >>> i.e, the same error as with MOPAC for the same system. Comparing with >>> the furnished Example1 - which ended OK also in my hands - I was unable to >>> catch which file corresponds to the "QM output file" charmm++ is >>> complaining about. >>> >>> Thanks for help >>> >>> francesco pietra >>> >> >> >
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