From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Thu Jan 19 2017 - 11:56:20 CST
Hi Marcelo:
What about colvars in the config.namd file (the same colvars that where
used in minimizing/heating/npt)? They are accepte and the simulation is
running. Actually these colvars are for the qm part, keeping a foreign
molecule near the transition metal atom, which might well be unreasonable
for a qm-mm.
thanks
francesco pietra
On Tue, Jan 17, 2017 at 10:58 PM, Marcelo C. R. Melo <melomcr_at_gmail.com>
wrote:
> 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 <(217)%20244-5983>
>
> 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
>>>>
>>>
>>>
>>
>
This archive was generated by hypermail 2.1.6 : Sun Dec 31 2017 - 23:21:00 CST