Dear Ross,
I agree with out that gradients are in general much more trustworthy and
informative than energies when it comes to implementations.
However, I really need the total potential energy like to one that I get
from the Orca PM3 output and not the heats of formations.
I would really like to find a way to do it within AMBER otherwise I will
have to give up using it.
Moreover, I noticed two more thing.
I use PLUMED2 to monitor some CVs during the simulation.
1) If one uses imin=5 reading an external trajectory with plumed=1 and a
plumed file, AMBER recognizes the presence of plumed and say it will use
it.
however, plumed is not called during the AMBER run with the external
trajectory and , thus, I had to grep the information I needed from the
AMBER output.
2) If AMBER prints only the heats of formation than there is a problem with
the plumed2 patch as plumed intends to read the potential energy and
instead it read the heats of formation.
From the plumed side we can modify the patch ubt we nedd to have access to
the potential energy from AMBER.
Lots of information, I am sorry for this long email.
Best,
Giovanni
Il giorno dom 3 feb 2019 alle ore 16:34 Ross Walker <ross.rosswalker.co.uk>
ha scritto:
> Hi Giovanni,
>
> I'd add that the final results in each case, which I believe is from the
> structure after a minimization step has been taken, match for the MM parts.
> You might want to try a couple of steps of minimization and see if that
> still holds. This suggests that while the SCF energies reported differ the
> gradients match. Note when trying to determine if there are differences in
> implementations it is much better to compare gradients than it is energies.
> I'd suggest dumping the force matrices after the first energy evaluation
> and comparing those.
>
> All the best
> Ross
>
> > On Feb 2, 2019, at 19:45, Goetz, Andreas <agoetz.sdsc.edu> wrote:
> >
> > 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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> >>>
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Received on Sun Feb 03 2019 - 10:00:03 PST
