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 - 04:30:02 PST
