AMBER Archive (2008)

Subject: Re: RE: AMBER: about QMMM output

From: linfu (linfu3200_at_mail.sioc.ac.cn)
Date: Fri Jul 04 2008 - 12:09:23 CDT

Thank you very much for profs. Ross and Gustavo's answer.
>Note that E(QM/MM)VDW is
>calculated classically and so this gets included in the general VDWaals
>energy term.
However, from tutorial http://amber.scripps.edu/tutorials/advanced/tutorial2/section4.htm
the result below shows
when NSTEP =0, in my opinion, sander hasn't started doing MD and just calculated energy(?)
at this time VDWAALS should be the same for Classical and QM/MM method, However,
they differ much in VDWAALS term (VDWAALS=930.8446 in classical and VDWAALS=881.6951 in QM/MM)

when NSTEP=1, it is understandable for the difference between VDWAALS term because 1 STEP of
MD simulation has done.

Classical

  NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 455.28 PRESS = 0.0
 Etot = -9086.7258 EKtot = 4144.0991 EPtot = -13230.8249
 BOND = 0.0650 ANGLE = 0.1616 DIHED = 2.5068
 1-4 NB = 1.1157 1-4 EEL = -19.4429 VDWAALS = 930.8446
 EELEC = -14146.0758 EHBOND = 0.0000 RESTRAINT = 0.0000
 Ewald error estimate: 0.1330E-03
 ------------------------------------------------------------------------------
 NSTEP = 1 TIME(PS) = 0.002 TEMP(K) = 346.22 PRESS = 0.0
 Etot = -10079.4435 EKtot = 3151.3814 EPtot = -13230.8249
 BOND = 0.0650 ANGLE = 0.1616 DIHED = 2.5068
 1-4 NB = 1.1157 1-4 EEL = -19.4429 VDWAALS = 930.8446
 EELEC = -14146.0758 EHBOND = 0.0000 RESTRAINT = 0.0000
 Ewald error estimate: 0.1330E-03
 ------------------------------------------------------------------------------
 
QMMM
 
 NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 455.28 PRESS = 0.0
 Etot = -9041.3222 EKtot = 4144.0991 EPtot = -13185.4213
 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 881.6951
 EELEC = -14012.9122 EHBOND = 0.0000 RESTRAINT = 0.0000
 PM3ESCF= -54.2042
 Ewald error estimate: 0.5641E-01
 ------------------------------------------------------------------------------
 NSTEP = 1 TIME(PS) = 0.002 TEMP(K) = 346.23 PRESS = 0.0
 Etot = -10033.9525 EKtot = 3151.4687 EPtot = -13185.4213
 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 881.6951
 EELEC = -14012.9122 EHBOND = 0.0000 RESTRAINT = 0.0000
 PM3ESCF= -54.2042
 Ewald error estimate: 0.5641E-01
------------------------------------------------------------------------------

Best Regards,
Lin

======= 2008-07-05 00:30:09 ฃบ=======

>Just to clarify some more here.
>
>The ESCF printed, for a QM/MM PME calculation, in the sander output file is:
>
>ESCF=E(QM)+E(QM/MM)ElecRS
>
>Where ElecRS refers to the real space QM/MM electrostatic interaction, i.e.
>what is inside the cut off, adjusted for Erfc. Note that E(QM/MM)VDW is
>calculated classically and so this gets included in the general VDWaals
>energy term.
>
>The QM/MM PME part of the electrostatics ends up in EELEC with the rest of
>the PME and MM/MM real space interactions.
>
>Gustavo is right that there are also certain covalent terms crossing the
>QM/MM boundary and they end up in the corresponding BOND, ANGLE etc terms.
>However, in your case the contributions would be zero here.
>
>I hope this helps, the papers Gustavo refers to will hopefully make it
>clear.
>
>All the best
>Ross
>
>> -----Original Message-----
>> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
>> Of Gustavo Seabra
>> Sent: Friday, July 04, 2008 8:33 AM
>> To: amber_at_scripps.edu
>> Subject: Re: AMBER: about QMMM output
>>
>> Yes and no ;-)
>>
>> That is the SCF energy, the energy from the QM calculation. This
>> energy is influenced by the presence of the MM atoms, so in a way you
>> can say it does include /some/ of the QM/MM electrostatic interaction
>> energy. However, the QM/MM interaction also has other terms, like van
>> der Waals and bond terms, which are not included there.
>>
>> For more details, see:
>> J. Phys. Chem. A (2007), 111, 5655-5664
>> J Comput Chem (2008), 29 1019จC1031
>>
>> HTH,
>> Gustavo.
>>
>> On Thu, Jul 3, 2008 at 10:40 PM, linfu <linfu3200_at_mail.sioc.ac.cn> wrote:
>> > Dear AMBER community!
>> >
>> > I have question about QMMM output. for example QM part use PM3
>> > In the output there is a energy term called PM3ESCF.
>> > Does PM3ESCF(ligand) = E<QM(ligand)>+E<QM(ligand)/MM(water+protein)> ?
>> > if the ligand has no covalent bond with protein and QM part is ligand.
>> >
>> > Thank you in advance!
>> >
>> >
>> > Best Regards,
>> > Lin
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