The Effective Fragment Molecular Orbital Method
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Transcript of The Effective Fragment Molecular Orbital Method
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The Effective Fragment Molecular OrbitalMethod
Casper Steinmann1 Dmitri G. Fedorov2 Jan H. Jensen1
1Department of Chemistry, University of Copenhagen, Denmark
2AIST, Umezono, Tsukuba, Ibaraki, Japan
September 14th, 2011
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Outline
1 Motivation
2 The Fragment Molecular Orbital Method
3 The Effective Fragment Potential Method
4 The Effective Fragment Molecular Orbital Method
5 Results
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Motivation
Treatment of Very Large Systems• We want quantum mechanics (QM) to do chemistry.
• We want the speed of force-fields (MM) to treat large systems.
Usually done via hybrid QM/MM methods
We propose a fragment based, on-the-fly parameterless polarizableforce-field.
• A merger between FMO and EFP.
• FMO: Faster FMO by the use of classical approximations
• EFP: Flexible EFP’s.
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FMO
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FMO2 Method
The two-body FMO2 method on a system of N fragments
EFMO =
N∑
I
EI +
N∑
I>J
(EIJ − EI − EJ ),
with fragment energies obtained as
EX = 〈ΨX |HX |ΨX〉
where
HX =∑
i∈X
−1
2∇2
i +
all∑
C
−ZC
|ri −RC |+∑
j>i
1
|ri − rj |+
all∑
K 6∈X
∫
ρK(r′)
|ri − r′|dr′
+ ENRX
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FMO2 MethodUsing a single Slater determinant to represent |ΨX〉, we obtain
fXφXk = ǫXk φX
k .
Here,fX = hX + V X + gX = hX + gX ,
where
V X =
all∑
C∈X
−ZC
|r1 −RC |+
all∑
K 6∈X
∫
ρK(r′)
|r1 − r′|dr′
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FMO2 Methodexpanding our molecular orbitals φ in a basis set
φXk =
∑
µ
CXµkχµ
we obtain, the Fock matrix elements of V X
V Xµν = 〈µ|V X |ν〉 =
all∑
K 6∈X
uKµν +
all∑
K 6∈X
υKµν
which are given as
uKµν = 〈µ|
∑
C∈K
−ZC
|r1 −RC ||ν〉,
andυKµν =
∑
λσ∈K
DKλσ(µν|λσ).
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FMO approximationsFMO2 formally scales as O(N2), wants to be O(N). We needdistance-based approximations:
RI,J = mini∈I,j∈J
|ri − rj |
rvdwi + rvdwj
• 1) Approximate ESP (Resppc):
uKµν =
∑
λσ∈K
DKλσ(µν|λσ) →
∑
C∈K
〈µ|QC
|r1 −RC ||ν〉
• 2) Approximate dimer interaction (Resdim):
EIJ ≈ EI+EJ+Tr(
DIuJ)
+Tr(
DJuI)
+∑∑
DIµνD
Jλσ(µν|λσ)
Usually, Resdim and Resppc are equal (2.0)
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A couple of pictures to help
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A couple of pictures to help
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Covalent Bonds in FMOIn FMO, bonds are detatched instead of capped.
BDA|-BAA
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HOP vs. AFOTwo methods in FMO: hybrid orbital projection (HOP) and adaptivefrozen orbitals (AFO)
Both modifies the Fock-operator
fX = hX + gX +∑
k
Bk|φ〉〈φ|
• HOP: External model system generated and used
• AFO: Generated on the fly automatically:
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AFO
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AFO
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AFO
We shall return to AFO later ...
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EFP
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EFPEFP is an approximation to the RHF interaction energy, Eint
Eint = ERHF −∑
I
E0I ≈ EEFP
The EFP energy
EEFP =∑
I>J
∆EEFPIJ + Eind
total
∆EEFPIJ = Ees
IJ + (ExrIJ + Ect
IJ )
EesIJ using distributed multipoles.
Eindtotal using induced dipoles based on distributed polarizabilities.
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EFPEFP is an approximation to the RHF interaction energy, Eint
Eint = ERHF −∑
I
E0I ≈ EEFP
The EFP energy
EEFP =∑
I>J
∆EEFPIJ + Eind
total
∆EEFPIJ = Ees
IJ + (ExrIJ + Ect
IJ )
EesIJ using distributed multipoles.
Eindtotal using induced dipoles based on distributed polarizabilities.
• The internal geometry is fixed.
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EFPEFP is an approximation to the RHF interaction energy, Eint
Eint = ERHF −∑
I
E0I ≈ EEFP
The EFP energy
EEFP =∑
I>J
∆EEFPIJ + Eind
total
∆EEFPIJ = Ees
IJ + (ExrIJ + Ect
IJ )
EesIJ using distributed multipoles.
Eindtotal using induced dipoles based on distributed polarizabilities.
• The internal geometry is fixed.
• You need to construct the EFP’s before you can use them
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EFMO
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What is the EFMO method?
You start with FMO ...• Remove the ESP
Now you have N gas phase calculations.
Then you mix in some EFP• Use EFP to describe many-body interactions
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EFMO RHF Energy
The two-body FMO2 method on a system of N fragments
EEFMO =∑
I
E0I −→ do MAKEFP
+
Resdim≥RI,J∑
IJ
(
E0IJ − E0
I − E0J − Eind
IJ
)
+
Resdim<RI,J∑
IJ
EesIJ
+ Eindtot ,
• QM: Gas phase RHF (and MP2) calculations
• MM: Interaction energies by Effective Fragment Potentials
* obtain E0I , q, µ and Ω and α from RHF via a fake MAKEFP run.
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A couple of pictures to help
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A couple of pictures to help
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Correlation in EFMOCorrelation as in FMO
E = EEFMO + ECOR.
Here ECOR is
ECOR =
N∑
I
ECORI +
RI,J<Rcor∑
IJ
(
ECORIJ − ECOR
I − ECORJ
)
.
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EFMO vs. EFP vs. FMO
EFMO vs. EFP• EFMO energy includes internal energy, i.e. total energy can be
obtained.
• Short range interactions are computed using QM.
we assume Eex and Ect are negligible when RI,J > Resdim.
EFMO vs. FMO• No ESP, i.e. one SCC iteration.
• Many-body interactions are entirely classical.
General EFMO considerations• Calculation of classical parameters on-the-fly.
• Every EFMO calculation requires re-evaluation of EFPparameters.
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Rigorous Analysis of Small Water Clusters• Water trimer: Estimate lower bound to energy error
• Water pentamer: Estimate upper bound to energy error
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Rigorous Analysis of Small Water TrimerKitaura-Morokuma energy analysis
∆3Eint 6-31G(d) 6-31++G(d)-1.9 kcal/mol -1.45 kcal/mol
Many-body terms ∆3Eind +∆3Exr +∆3Ect +∆3EMIX
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Rigorous Analysis of Small Water TrimerKitaura-Morokuma energy analysis
∆3Eint 6-31G(d) 6-31++G(d)-1.9 kcal/mol -1.45 kcal/mol
Many-body terms ∆3Eind +∆3Exr +∆3Ect +∆3EMIX
∆3Eind 6-31G(d) 6-31++G(d)-0.9 kcal/mol -1.67 kcal/mol
EFMO error 1.0 kcal/mol -0.22 kcal/mol
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Rigorous Analysis of Small Water TrimerKitaura-Morokuma energy analysis
∆3Eint 6-31G(d) 6-31++G(d)-1.9 kcal/mol -1.45 kcal/mol
Many-body terms ∆3Eind +∆3Exr +∆3Ect +∆3EMIX
∆3Eind 6-31G(d) 6-31++G(d)-0.9 kcal/mol -1.67 kcal/mol
EFMO error 1.0 kcal/mol -0.22 kcal/mol
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Rigorous Analysis of Small Water TrimerKitaura-Morokuma energy analysis
∆3Eint 6-31G(d) 6-31++G(d)-1.9 kcal/mol -1.45 kcal/mol
Many-body terms ∆3Eind +∆3Exr +∆3Ect +∆3EMIX
∆3Eind 6-31G(d) 6-31++G(d)-0.9 kcal/mol -1.67 kcal/mol
EFMO error 1.0 kcal/mol -0.22 kcal/mol
6-31G(d):• Lower bound to the error in energy is ≈ 0.33 kcal/mol/HB
6-31++G(d):• Lower bound to the error in energy is ≈ -0.07 kcal/mol/HB
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Rigorous Analysis of Small Water PentamerKitaura-Morokuma energy analysis
∆nEint 6-31G(d) 6-31++G(d)-6.10 kcal/mol -5.14 kcal/mol
Many-body terms ∆nEind +∆nEEX +∆nECT +∆nEMIX
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Rigorous Analysis of Small Water PentamerKitaura-Morokuma energy analysis
∆nEint 6-31G(d) 6-31++G(d)-6.10 kcal/mol -5.14 kcal/mol
Many-body terms ∆nEind +∆nEEX +∆nECT +∆nEMIX
∆nEind 6-31G(d) 6-31++G(d)-1.97 kcal/mol -3.68 kcal/mol
EFMO error -4.13 kcal/mol -1.46 kcal/mol
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Rigorous Analysis of Small Water PentamerKitaura-Morokuma energy analysis
∆nEint 6-31G(d) 6-31++G(d)-6.10 kcal/mol -5.14 kcal/mol
Many-body terms ∆nEind +∆nEEX +∆nECT +∆nEMIX
∆nEind 6-31G(d) 6-31++G(d)-1.97 kcal/mol -3.68 kcal/mol
EFMO error -4.13 kcal/mol -1.46 kcal/mol
6-31G(d):• Upper bound to the error in energy is ≈ 1.03 kcal/mol/HB
6-31++G(d):• Upper bound to the error in energy is ≈ 0.37 kcal/mol/HB
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Rigorous analysis of Small Water Clusters6-31G(d):
• Lower bound to the error in energy is ≈ 0.33 kcal/mol/HB• Upper bound to the error in energy is ≈ 1.03 kcal/mol/HB
6-31++G(d):• Lower bound to the error in energy is ≈ -0.07 kcal/mol/HB• Upper bound to the error in energy is ≈ 0.37 kcal/mol/HB
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20 water molecule clusters
6-31G(d) ∆E [kcal/mol/HB] [kcal/mol] Resdim = 2.0EFMO 0.53 15.8FMO2 -0.39 -11.6
6-31++G(d)EFMO -0.08 -2.5FMO2 -0.76 -21.8
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EFMO Gradient
∂EEFMO
∂xI
=∑
I
∂
∂xI
E0I
+
RI,J≤Rcut∑
I>J
(
∂
∂xI
∆E0IJ −
∂
∂xI
EindIJ
)
+
RI,J>Rcut∑
I>J
∂
∂xI
EesIJ +
∂
∂xI
Eindtotal + TM
xI
TMI is the contribution to the gradient on atom I due to torques
arising from nearby atoms.
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EFMO Gradient• For water clusters, ∇XI
EEFMOa − EEFMO
n ≈ 10−4 Hartree / Bohr
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EFMO Gradient• For water clusters, ∇XI
EEFMOa − EEFMO
n ≈ 10−4 Hartree / Bohr
"Those are not good gradients."
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Wait until you see the covalently bonded systems then.
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EFMO for Covalent Systems
Covalent systems pose a problem in EFMO because ...• ... Inherent close (and even overlapping) electrostatics.
• ... Inherent close position of polarizable points and nearbyelectrostatics.
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Back to the drawing board
C1 C
H
H
H
H
C5
H
H
C C
H
HHH
HH
+
a) b) c)
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Back to the drawing board• 1) The frozen orbital (during the SCF) is allowed to mix during
Foster-Boys localization.
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Back to the drawing board• 1) The frozen orbital (during the SCF) is allowed to mix during
Foster-Boys localization.• 1) Crap. Errors ≈ 50 kcal/mol. FMO2: ≈ 5 kcal/mol
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Back to the drawing board• 1) The frozen orbital (during the SCF) is allowed to mix during
Foster-Boys localization.• 1) Crap. Errors ≈ 50 kcal/mol. FMO2: ≈ 5 kcal/mol
• 2) The localized orbital is kept frozen, i.e. as it is during the SCF.
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Back to the drawing board• 1) The frozen orbital (during the SCF) is allowed to mix during
Foster-Boys localization.• 1) Crap. Errors ≈ 50 kcal/mol. FMO2: ≈ 5 kcal/mol
• 2) The localized orbital is kept frozen, i.e. as it is during the SCF.• 2) Works, Errors grows with system size and are on-par with
FMO2. Requires much more screening.
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Energies for Conformers of Polypeptides
k(R, α, β) = 1− exp(
−√
αβ|R|2)(
1 +√
αβ|R|2)
AM,X =1
N
N∑
I
∣
∣EMI − EX
I
∣
∣ .
0.1 0.2 0.3 0.4 0.5 0.6
2
4
6
8
10
12
AEFMO,X
[kca
l/mol
]
Peptide MAD for EFMO/2 vs. Screening Parameter
P1(RHF)P1(MP2)P2(RHF)P2(MP2)P3(RHF)P3(MP2)
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Energies for Conformers of Polypeptides
k(R, α, β) = 1− exp(
−√
αβ|R|2)(
1 +√
αβ|R|2)
AM,X =1
N
N∑
I
∣
∣EMI − EX
I
∣
∣ .
P1 P2 P30
1
2
3
4
5
6
7
8
AM,X
[kca
l/mol
]
Peptide MAD for 2 Residues per Fragment
FMO2-RHF/HOPFMO2-MP2/HOPFMO2-RHF/AFOFMO2-MP2/AFOEFMO-RHFEFMO-MP2
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Energies for Proteins
Table: Energy Error of EFMO and FMO2/AFO compared to ab initiocalculations on proteins using two residues per fragment.
Nres EFMO FMO2/AFO
Rcut = 2.0 Rcut = 2.0
RHF MP2 RHF MP2
1L2Y 20 3.2 -4.3 1.7 6.41UAO 10 1.8 1.5 0.4 1.4
• Timings: 5 times faster than FMO2.
• Requires lots of screening.
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Back to the drawing board• The backbone is the main problem.
• Errors around 10−3(10−4) Hartree / Bohr
• Timings: 1.5 times faster than FMO2-MP2
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Timings
5 10 15 20 25 30 35 40Total CPU count
5
10
15
20
25
30
35
40
Gain
-Fac
tor i
n CP
U w
allti
me
Gain-Factor in CPU walltime for increasing CPU count
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Summary• Successful merger of the FMO and EFP method
• For molecular clusters, it performer pretty good.
• For systems with covalent bonds, work is needed.
• Faster than FMO2, roughly same accuracy.
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Outlook• EFMO-PCM (meeting with Hui Li tomorrow)
• EFMO QM/MM (Based on FMO/FD)
• More EFP, less QM (Spencer Pruitt)
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AcknowledgementsJan H. JensenDmitri G. Fedorov
Bad Boys of Quantum Chemistry:Anders ChristensenMikael W. Ibsen (FragIt)Luca De Vico (FragIt)Kasper Thofte
$$ - Insilico Rational Engineering of Novel Enzymes (IRENE)
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Thank you for your attention
proteinsandwavefunctions.blogspot.com
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Gradient Contribution
JK
I
dvdu
dw
IuvII
II
r
r1
2
dwmA = −dum
A − dvmA
dumA = wA (τmA · vA)+uA×wA (τmA ·wA)
dvmA = −wA (τmA · uA)+vA×wA (τmA ·wA)
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