Hi Erdem,
thanks for correcting the energy term in the eq. the equation should have
been
EMMdihedral = (PK/IDIVF) * (1 + cos(PN*phi – PHASE)) EQ.1
and the EQM energy is rectified (EQMr) by substracting EMM (computed
by zeroing Vn parameters for the dihedral of interest) from EQM to
yield a a final EQMr curve , to which we fit the EMM curve.
EQMr= EQM - EMM(with zero dihedral parameter of interest) EQ.2
Having said that, my question was
whether or not QM potential energies computed by paramfit are rectified by EQ.2.
If not, do we need to rectify it manually? or Do we really need to
rectify it as in EQ.2.
best,
Cenk
On Wed, Sep 7, 2022 at 12:51 PM Erdem Yeler <erdemyeler.gmail.com> wrote:
> I think you are confused : in quantum_A.dat, you should put quantum
> energies not MM energies. (PK/IDIVF) * (1 + cos(PN*phi – PHASE)) is a MM
> energy NOT QM Energy.
> All the best,
> Erdem
> Istanbul Technıcal University
> Department of Chemistry
>
>
>
> Cenk Andac via AMBER <amber.ambermd.org>, 6 Eyl 2022 Sal, 18:16 tarihinde
> şunu yazdı:
>
>> Dear Amber community,
>>
>> I have been working on dihedral parameters development using paramfit.
>> I have a simple question.
>> In developing AMBER dihedral parameters the following EQ is used.
>>
>> Edihedral = EQM - EVDW-ELE(MM) = (PK/IDIVF) * (1 + cos(PN*phi – PHASE))
>>
>> here
>> Edihedral = EQM - EVDW-ELE(MM)
>>
>> I was wondering when running paramfit with -q quantum_A.dat
>>
>> what kind of QM energies I need to use in
>> quantum_A.dat, Edihedral or EQM ?
>>
>> thanks in advance,
>>
>> best
>>
>> Cenk Andac
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>>
>
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Received on Wed Sep 07 2022 - 06:00:03 PDT
