Hi Giovanni,
Perhaps the energy difference is due to different natural constants in Amber and Orca. Can you extract the QM region for those snapshots or use mechanical embedding and then check energy differences with Amber/sqm and Amber/Orca? This will clarify whether the energy difference you observe is due to QM/MM electronic embedding.
Also note that Amber outputs energy in kcal/mol so the difference is around 3 kcal/mol (not kJ/mol).
All the best,
Andy
—
Dr. Andreas W. Goetz
Assistant Research Scientist
San Diego Supercomputer Center
Tel: +1-858-822-4771
Email: agoetz.sdsc.edu
Web: www.awgoetz.de
> On Feb 2, 2019, at 4:08 AM, GiovanniMaria Piccini <giovannimaria.piccini.gmail.com> wrote:
>
> Hi Andy,
>
> thank you for your quick and enlightening reply.
>
> However, I still observe a difference when comparing the energy of two
> consecutive snapshots.
> Below I report the data.
>
> AMBER PM3
>
> FINAL RESULTS
>
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 -5.1000E+03 1.3733E+01 5.9035E+01 C 1
>
> BOND = 0.0000 ANGLE = 0.0000 DIHED =
> 0.0000
> VDWAALS = 771.4407 EEL = -5669.3000 HBOND =
> 0.0000
> 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
> 0.0000
> PM3ESCF = -202.1858
> minimization completed, ENE= -.51000451E+04 RMS= 0.137329E+02
> minimizing coord set # 2
>
>
> Maximum number of minimization cycles reached.
>
>
> FINAL RESULTS
>
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 -5.2021E+03 1.3595E+01 6.2275E+01 O 1624
>
> BOND = 0.0000 ANGLE = 0.0000 DIHED =
> 0.0000
> VDWAALS = 749.4332 EEL = -5662.0943 HBOND =
> 0.0000
> 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
> 0.0000
> PM3ESCF = -289.4349
> minimization completed, ENE= -.52020961E+04 RMS= 0.135950E+02
> minimizing coord set # 3
>
>
> Energy difference = (-5.2021+5.1000)*10^3 = -102.1000
>
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
> Orca PM3
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 -2.6309E+04 1.3753E+01 5.7750E+01 O 280
>
> BOND = 0.0000 ANGLE = 0.0000 DIHED =
> 0.0000
> VDWAALS = 771.4407 EEL = -5669.3000 HBOND =
> 0.0000
> 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
> 0.0000
> EXTERNESCF = -21411.2247
> minimization completed, ENE= -.26309084E+05 RMS= 0.137530E+02
> minimizing coord set # 2
>
>
> Maximum number of minimization cycles reached.
>
>
> FINAL RESULTS
>
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 -2.6414E+04 1.3626E+01 6.2275E+01 O 1624
>
> BOND = 0.0000 ANGLE = 0.0000 DIHED =
> 0.0000
> VDWAALS = 749.4332 EEL = -5662.0943 HBOND =
> 0.0000
> 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
> 0.0000
> EXTERNESCF = -21501.8068
> minimization completed, ENE= -.26414468E+05 RMS= 0.136257E+02
> minimizing coord set # 3
>
>
> Energy difference = (-2.6414+2.6309)*10^4 = -105.0000
>
>
> As you can see I still observe a difference of about 3 kJ/mol but maybe
> this is due to a slightly different treatment of the electrostatic
> embedding.
>
> Besides that, it would be really helpful for me to have the same kind of
> energy in the AMBER output whether heats of formation of electronic +
> core-core repulsion energy.
> Is there a way I can do that by modifying a line in the qmmm AMBER module?
> Alternatively, can I reconstruct one of the two quantities just from the
> AMBER or Orca outputs?
>
> Thanks again.
>
> Best,
> Giovanni
>
> Il giorno ven 1 feb 2019 alle ore 20:15 Goetz, Andreas <agoetz.sdsc.edu> ha
> scritto:
>
>> Hi Giovanni,
>>
>> Semiempirical QM energies in Amber (sqm and QM/MM via sander) are heats of
>> formation. Orca instead reports the total electronic energy (including core
>> repulsion). Hence what you observe should be the difference between
>> electronic energy and heat of formation. The energy difference between two
>> snapshots should be identical.
>>
>> All the best,
>> Andy
>>
>> —
>> Dr. Andreas W. Goetz
>> Assistant Research Scientist
>> San Diego Supercomputer Center
>> Tel: +1-858-822-4771
>> Email: agoetz.sdsc.edu
>> Web: www.awgoetz.de
>>
>>> On Feb 1, 2019, at 8:55 AM, GiovanniMaria Piccini <
>> giovannimaria.piccini.gmail.com> wrote:
>>>
>>> Dear all,
>>>
>>> I have noticed large differences between the semiempirical energies
>> between
>>> AMBER internal PM3 and Orca PM3 used as external QM potentail.
>>> Here I report the results of a single point energy evaluation given an
>>> external trajectory, i.e. the same structure is evaluated.
>>> I use the same parameters for the two calculations that differ only for
>> the
>>> way the QM part is calculated (see below).
>>>
>>> AMBER PM3:
>>>
>>> FINAL RESULTS
>>>
>>>
>>>
>>> NSTEP ENERGY RMS GMAX NAME NUMBER
>>> 1 -5.1000E+03 1.3733E+01 5.9035E+01 C 1
>>>
>>> BOND = 0.0000 ANGLE = 0.0000 DIHED =
>>> 0.0000
>>> VDWAALS = 771.4407 EEL = -5669.3000 HBOND =
>>> 0.0000
>>> 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
>>> 0.0000
>>> PM3ESCF = -202.1858
>>> minimization completed, ENE= -.51000451E+04 RMS= 0.137329E+02
>>> minimizing coord set # 2
>>>
>>>
>>> AMBER/Orca PM3
>>>
>>> FINAL RESULTS
>>>
>>>
>>>
>>> NSTEP ENERGY RMS GMAX NAME NUMBER
>>> 1 -2.6309E+04 1.3753E+01 5.7750E+01 O 280
>>>
>>> BOND = 0.0000 ANGLE = 0.0000 DIHED =
>>> 0.0000
>>> VDWAALS = 771.4407 EEL = -5669.3000 HBOND =
>>> 0.0000
>>> 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
>>> 0.0000
>>> EXTERNESCF = -21411.2247
>>> minimization completed, ENE= -.26309084E+05 RMS= 0.137530E+02
>>> minimizing coord set # 2
>>>
>>>
>>> The two input read:
>>>
>>> AMBER PM3:
>>>
>>> Production
>>> &cntrl
>>> imin=5,
>>> maxcyc=1,
>>> ntx=1,
>>> ntpr=1,
>>> ntwx=1,
>>> cut=8.0,
>>> ntb=1,
>>> ntp=0,
>>> ntt=3,
>>> gamma_ln=2.0,
>>> ig=-1,
>>> ifqnt=1,
>>> plumed=1,
>>> plumedfile='plumed.dat'
>>> /
>>> &qmmm
>>> qmmask='.1-6',
>>> qmcharge=-1,
>>> qm_theory='PM3',
>>> qmshake=1,
>>> qm_ewald=0,
>>> qmmm_int=1
>>> /
>>>
>>> AMBER/Orca PM3:
>>>
>>> Production
>>> &cntrl
>>> imin=5,
>>> maxcyc=1,
>>> ntx=1,
>>> ntpr=1,
>>> ntwx=1,
>>> cut=8.0,
>>> ntb=1,
>>> ntp=0,
>>> ntt=3,
>>> gamma_ln=2.0,
>>> ig=-1,
>>> ifqnt=1,
>>> plumed=1,
>>> plumedfile='plumed.dat'
>>> /
>>> &qmmm
>>> qmmask='.1-6',
>>> qmcharge=-1,
>>> qm_theory='EXTERN',
>>> qmshake=1,
>>> qm_ewald=0,
>>> qmmm_int=1
>>> /
>>>
>>> &orc
>>> method ='pm3',
>>> basis ='svp',
>>> convkey='TIGHTSCF',
>>> /
>>>
>>> As it can be observed there is an order of magnitude difference between
>> the
>>> two energies and this depends, I believe, on the QM energy.
>>> May it also be the subtractive scheme?
>>> I need to fix this because when have to use DFT method with Orca and
>>> compare them with AMBER semiempirical I must be sure I am comparing the
>>> same quantities.
>>>
>>> I am using AMBER 17 and Orca/4.0.0
>>>
>>> Thank you in advance,
>>> Giovanni
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Sat Feb 02 2019 - 17:00:01 PST
