path integral molecular dynamics ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfpath...
TRANSCRIPT
![Page 1: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/1.jpg)
PATH INTEGRAL MOLECULAR DYNAMICS:APPLICATIONS & NEW ALGORITHMS.
Alejandro Perez PazNano-bio Spectroscopy Group
University of the Basque CountrySpain
IPAM CCS WorkshopLos Angeles, CA
May 18, 2011
![Page 2: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/2.jpg)
Outline
I Introduction to Path Integrals (PI)I Double proton transfer in DNA base pair modelsI Development of free energy methods in PIMDI Improving the convergence of PIMDI Summary
![Page 3: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/3.jpg)
![Page 4: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/4.jpg)
Outline
Introduction to Path Integrals
Double proton transfer in DNA base pair models
Development of free energy methods in PIMD
Improving the convergence of PIMD
Summary
![Page 5: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/5.jpg)
Quantum Mechanics in Nature
What can PI do for you?
I DelocalizationI Zero Point Energy (ZPE)I TunnelingI Theory development (QCD)I quantum dynamics? R. P. Feynman
www.wikipedia.org JCP 130, 184105 (2009).
![Page 6: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/6.jpg)
PI Formulation of Canonical Partition Function
The canonical density matrix operator
ρ (β) = exp (−βH) ,
where H = T + U and [T,U] 6= 0.
Z (β) = Tr(
e−βH)
=
∫dx1〈x1|e−β(T+U)|x1〉 = lim
P→∞
∫dx1〈x1|ΩP|x1〉,
where Ω = e−β2P Ue−
βP Te−
β2P U, which follows from Trotter
theorem1
e−β(T+U) = limP→∞
[e−
β2P Ue−
βP Te−
β2P U]P.
1Tuckerman, Stat. Mech.: Theory & Molecular Simulation, Oxford, 2010
![Page 7: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/7.jpg)
PI Formulation of Canonical Partition Function
The canonical density matrix operator
ρ (β) = exp (−βH) ,
where H = T + U and [T,U] 6= 0.
Z (β) = Tr(
e−βH)
=
∫dx1〈x1|e−β(T+U)|x1〉 = lim
P→∞
∫dx1〈x1|ΩP|x1〉,
where Ω = e−β2P Ue−
βP Te−
β2P U, which follows from Trotter
theorem1
e−β(T+U) = limP→∞
[e−
β2P Ue−
βP Te−
β2P U]P.
1Tuckerman, Stat. Mech.: Theory & Molecular Simulation, Oxford, 2010
![Page 8: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/8.jpg)
Inserting (P− 1) completeness relations I =∫
dx|x〉〈x|
Z(β) = limP→∞
∫dx1dx2 · · · dxP〈x1|Ω|x2〉〈x2|Ω|x3〉 · · · 〈xP|Ω|x1〉
= limP→∞
∫ P∏i=1
dxi〈xi|Ω|xi+1〉|xP+1=x1 .
Need to compute
〈xi|Ω|xi+1〉 = 〈xi|e−β2P Ue−
βP Te−
β2P U|xi+1〉
= e−β2P
[U(xi)+U(xi+1)
]〈xi|e−
βP T |xi+1〉.
What can we do...?
![Page 9: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/9.jpg)
Inserting (P− 1) completeness relations I =∫
dx|x〉〈x|
Z(β) = limP→∞
∫dx1dx2 · · · dxP〈x1|Ω|x2〉〈x2|Ω|x3〉 · · · 〈xP|Ω|x1〉
= limP→∞
∫ P∏i=1
dxi〈xi|Ω|xi+1〉|xP+1=x1 .
Need to compute
〈xi|Ω|xi+1〉 = 〈xi|e−β2P Ue−
βP Te−
β2P U|xi+1〉
= e−β2P
[U(xi)+U(xi+1)
]〈xi|e−
βP T |xi+1〉.
What can we do...?
![Page 10: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/10.jpg)
Inserting (P− 1) completeness relations I =∫
dx|x〉〈x|
Z(β) = limP→∞
∫dx1dx2 · · · dxP〈x1|Ω|x2〉〈x2|Ω|x3〉 · · · 〈xP|Ω|x1〉
= limP→∞
∫ P∏i=1
dxi〈xi|Ω|xi+1〉|xP+1=x1 .
Need to compute
〈xi|Ω|xi+1〉 = 〈xi|e−β2P Ue−
βP Te−
β2P U|xi+1〉
= e−β2P
[U(xi)+U(xi+1)
]〈xi|e−
βP T |xi+1〉.
What can we do...?
![Page 11: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/11.jpg)
Introduce complete set momentum eigenstates I =∫
dp|p〉〈p|
〈xi|e−βP T |xi+1〉 =
∫dp〈xi|p〉〈p|e−
βP T |xi+1〉 =
∫dpe−βp2/2mP〈xi|p〉〈p|xi+1〉.
Now use 〈x|p〉 = 1√2π~
eipx/~ in previous equality
12π~
∫dp e−
β2mP p2
eip(xi−xi+1)/~ =
√mP
2πβ~2 e− mP
2β~2 (xi+1−xi)2
,
where we have completed the square in the last expression.
![Page 12: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/12.jpg)
Introduce complete set momentum eigenstates I =∫
dp|p〉〈p|
〈xi|e−βP T |xi+1〉 =
∫dp〈xi|p〉〈p|e−
βP T |xi+1〉 =
∫dpe−βp2/2mP〈xi|p〉〈p|xi+1〉.
Now use 〈x|p〉 = 1√2π~
eipx/~ in previous equality
12π~
∫dp e−
β2mP p2
eip(xi−xi+1)/~ =
√mP
2πβ~2 e− mP
2β~2 (xi+1−xi)2
,
where we have completed the square in the last expression.
![Page 13: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/13.jpg)
Introduce complete set momentum eigenstates I =∫
dp|p〉〈p|
〈xi|e−βP T |xi+1〉 =
∫dp〈xi|p〉〈p|e−
βP T |xi+1〉 =
∫dpe−βp2/2mP〈xi|p〉〈p|xi+1〉.
Now use 〈x|p〉 = 1√2π~
eipx/~ in previous equality
12π~
∫dp e−
β2mP p2
eip(xi−xi+1)/~ =
√mP
2πβ~2 e− mP
2β~2 (xi+1−xi)2
,
where we have completed the square in the last expression.
![Page 14: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/14.jpg)
Then, we obtain
〈xi|Ω|xi+1〉 =
√mP
2πβ~2 e− mP
2β~2 (xi+1−xi)2− β
2P [U(xi)+U(xi+1)].
Path integral representation of canonical quantum PF
Z (β) = limP→∞
(mP
2πβ~2
)P/2 ∫xP+1=x1
dx1 · · · dxP e−βUeff ,
where Ueff =∑P
i=1
[mP
2β2~2 (xi+1 − xi)2 + 1
P U (xi)].
Each quantum particle is mapped onto a collection of Pinteracting quasi-particles.11Chandler & Wolynes, JCP 74 4078 (1981).
![Page 15: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/15.jpg)
Then, we obtain
〈xi|Ω|xi+1〉 =
√mP
2πβ~2 e− mP
2β~2 (xi+1−xi)2− β
2P [U(xi)+U(xi+1)].
Path integral representation of canonical quantum PF
Z (β) = limP→∞
(mP
2πβ~2
)P/2 ∫xP+1=x1
dx1 · · · dxP e−βUeff ,
where Ueff =∑P
i=1
[mP
2β2~2 (xi+1 − xi)2 + 1
P U (xi)].
Each quantum particle is mapped onto a collection of Pinteracting quasi-particles.11Chandler & Wolynes, JCP 74 4078 (1981).
![Page 16: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/16.jpg)
The ring-polymer isomorphism
Analytical solutions to path integrals are limited:devise numerical techniques for complex systems.Discretized version of the path integral quantum PF:
Z(β) = limP→∞
(mP
2πβ~2
)P/2 ∫dx1 · · · dxP e
−β∑P
i=1
[m2 ω
2P(xi−xi+1)2+
U(xi)P
],
where ω2P = P/ (β~)2 and xP+1 = x1.
A quantum particle ismapped onto a collection ofP “beads” coupled viaharmonic springs & eachunder external potentialU/P.
centroid xc = 1P
∑Pi=1 xi
![Page 17: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/17.jpg)
The ring-polymer isomorphism
Analytical solutions to path integrals are limited:devise numerical techniques for complex systems.Discretized version of the path integral quantum PF:
Z(β) = limP→∞
(mP
2πβ~2
)P/2 ∫dx1 · · · dxP e
−β∑P
i=1
[m2 ω
2P(xi−xi+1)2+
U(xi)P
],
where ω2P = P/ (β~)2 and xP+1 = x1.
A quantum particle ismapped onto a collection ofP “beads” coupled viaharmonic springs & eachunder external potentialU/P.
centroid xc = 1P
∑Pi=1 xi
![Page 18: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/18.jpg)
The ring-polymer isomorphism
Introducing nuclear quantum effects with the ring polymer.
www.telluridescience.org/TullyLectures/tully.pdf
![Page 19: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/19.jpg)
PIMD Implementation
Assuming ergodicity, sampling can be effected using MD.Introduce a set of uncoupled Gaussian integrals to enablesampling of phase space (fictitious m′k)
Z(β) ≈ N∫
dp1 · · · dpP dx1 · · · dxP e−β∑P
k=1
[p2k
2m′k+ m
2 ω2P(xk−xk+1)2+ 1
P U(xk)
].
I Remember: Time is only a parameter for the exploration ofphase space (unphysical dynamics).
I Naive PIMD implementation suffers from non-ergodicity &multiple time scales issues1.
1 Hall & Berne, JCP 81 3641 (1984).
![Page 20: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/20.jpg)
Efficient PIMD ImplementationSolution M. Tuckerman et al. JCP 99 2796 (1993).
I Transformation coordinates:normal modes uk = 1√
P
∑Pj=1 xje2πi(j−1)(k−1)/P (centroid is u1)
or staging u1 = x1, uk = xk − (k−1)xk+1+x1k , k = 2, · · · ,P.
H (u,p) =
P∑k=1
[p2
k2m′k
+mk
2ω2
Pu2k +
1P
U (xk (u))
],
where m1 = 0. mk = kk−1 m for staging and
mk = 2mP [1− cos (2π(k − 1)/P)] for normal modes.I Fictitious masses chosen to collapse all time scales
m′1 = m, m′k = mk
I Massive thermostatsAlthough computationally intensive, PIMD can be parallelizedextremely well.
![Page 21: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/21.jpg)
Efficient PIMD ImplementationSolution M. Tuckerman et al. JCP 99 2796 (1993).
I Transformation coordinates:normal modes uk = 1√
P
∑Pj=1 xje2πi(j−1)(k−1)/P (centroid is u1)
or staging u1 = x1, uk = xk − (k−1)xk+1+x1k , k = 2, · · · ,P.
H (u,p) =
P∑k=1
[p2
k2m′k
+mk
2ω2
Pu2k +
1P
U (xk (u))
],
where m1 = 0. mk = kk−1 m for staging and
mk = 2mP [1− cos (2π(k − 1)/P)] for normal modes.I Fictitious masses chosen to collapse all time scales
m′1 = m, m′k = mk
I Massive thermostatsAlthough computationally intensive, PIMD can be parallelizedextremely well.
![Page 22: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/22.jpg)
Outline
Introduction to Path Integrals
Double proton transfer in DNA base pair models
Development of free energy methods in PIMD
Improving the convergence of PIMD
Summary
![Page 23: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/23.jpg)
Proton transfer reactions
Ubiquitous and crucial process in nature
S1 − H∗ · · · S2 ⇐⇒ S1 · · ·H∗ − S2
I Quantum Effects can be important even at roomtemperature!1
I Rearrangement of chemical bonds calls for ab initiodescription of the electronic part
1 Tuckerman & Marx, PRL 86 4946 (2001).
![Page 24: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/24.jpg)
Intermolecular proton transferDNA base pairs
I “Rare” tautomers implicated in DNA mutationsI Proton tunneling was hypothesized to favor “rare”
tautomers1
I Experimental evidence only for analogues (large KIE)2
1 Lowdin, RMP 35 724 (1963). 2 Zewail et al., Nature 378 260 (1995).
![Page 25: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/25.jpg)
Intermolecular proton transferDNA base pairs
I “Rare” tautomers implicated in DNA mutationsI Proton tunneling was hypothesized to favor “rare”
tautomers1
I Experimental evidence only for analogues (large KIE)2
1 Lowdin, RMP 35 724 (1963). 2 Zewail et al., Nature 378 260 (1995).
![Page 26: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/26.jpg)
Experiment on 7-azaindole dimer(g)
Douhal, Kim, & Zewail et al., Nature 378 260 (1995).
![Page 29: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/29.jpg)
Intermolecular double proton transfer
Formamidine-Formamide (FIFA) tautomer complex1
I Model system for A-T DNA base pairI Concerted mechanism.
1 J. Leszczynski et al., JPCA 106 12103 (2002)
![Page 30: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/30.jpg)
Intermolecular double proton transfer
Model for G-C DNA base pair
![Page 31: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/31.jpg)
Forces from “First Principles”
Combining the best of two worlds...
I The quantumnature of nuclei isdescribed usingthe PI formalism
I The electronicpart (governinginteractionbetween nuclei)is approximatedusing DFT
Car & Parrinello Molecular Dynamics (CPMD), PRL 55 2471 (1985).
![Page 32: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/32.jpg)
Forces from “First Principles”
Combining the best of two worlds...
I The quantumnature of nuclei isdescribed usingthe PI formalism
I The electronicpart (governinginteractionbetween nuclei)is approximatedusing DFT
Car & Parrinello Molecular Dynamics (CPMD), PRL 55 2471 (1985).
![Page 33: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/33.jpg)
Choice of DFT XC functional
Energetics (kcal/mol) from TURBOMOLE code/TZVPP basis set.Structures correspond ≈ to reactants (R), the transition state(TS), and products (P)
GC model AT modelmethod ∆EP−R ∆ETS−P ∆ETS−R ∆EP−R ∆ETS−P ∆ETS−R
RHF 13.50 14.65 28.15 11.80 9.47 21.27MP2 9.37 4.04 13.41 8.62 4.37 12.99CC2 10.24 2.67 12.91 9.24 3.08 12.32PBE0 10.95 3.00 13.95 8.93 2.81 11.74PBE 10.63 0.55 11.18 8.56 1.19 9.75B3LYP 11.39 4.78 16.17 9.47 3.52 12.99BLYP 11.16 3.15 14.31 9.30 2.44 11.74
BLYP represents best compromise between accuracy and cost!
![Page 34: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/34.jpg)
Free energy methods & rare events
I Reaction coordinate: ξ(r) = dHN − dHO
I Umbrella sampling1 and WHAM technique2
I Drive system along reaction coordinate using harmonicbias potential (centroid)3 ξc = 1
P∑P
i=1 ξi
1 Torrie & Valleau, Chem. Phys. Lett. 28 578 (1974)2 Ferrendberg & Swendsen, Phys. Rev. Lett. 61 2635 (1988)3 Gillan, PRL 58 563 (1987). Voth, JCP 97 8365 (1993).
![Page 35: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/35.jpg)
Free Energy Profiles Double Proton Transfer
Nuclear quantum effects have a dramatic impact on free energyprofiles.
Rare tautomers predicted dynamically unstable:therefore, not involved in mutations!
![Page 36: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/36.jpg)
Free Energy Profiles Double Proton Transfer
J. AM. CHEM. SOC. 132, 11510 (2010).
www.youtube.com
![Page 37: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/37.jpg)
![Page 38: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/38.jpg)
Outline
Introduction to Path Integrals
Double proton transfer in DNA base pair models
Development of free energy methods in PIMD
Improving the convergence of PIMD
Summary
![Page 39: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/39.jpg)
Computing Thermodynamic Quantities: Estimators
An estimator: function whose average approximates a physicalobservable.
Example: E(β) = − ∂∂β ln Z(β)
〈E〉 ≈ 1ZP
(mP
2πβ~2
)P/2 ∫dx1 · · · dxP εprim e−β
∑Pk=1
[m2 ω
2P(xk−xk+1)2+
U(xk)P
],
where the primitive estimator for energy is
εprim =P
2β+
P∑k=1
[U(xk)
P− m
2ω2
P(xk − xk+1)2]
xP+1=x1
.
Use MC, MD to sample this configuration integral.A more efficient estimator (virial) was proposed:Herman et al JCP 76 5150 (1982).
![Page 40: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/40.jpg)
Computing Thermodynamic Quantities: Estimators
An estimator: function whose average approximates a physicalobservable. Example: E(β) = − ∂
∂β ln Z(β)
〈E〉 ≈ 1ZP
(mP
2πβ~2
)P/2 ∫dx1 · · · dxP εprim e−β
∑Pk=1
[m2 ω
2P(xk−xk+1)2+
U(xk)P
],
where the primitive estimator for energy is
εprim =P
2β+
P∑k=1
[U(xk)
P− m
2ω2
P(xk − xk+1)2]
xP+1=x1
.
Use MC, MD to sample this configuration integral.A more efficient estimator (virial) was proposed:Herman et al JCP 76 5150 (1982).
![Page 41: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/41.jpg)
Internal Energy: Virial vs Primitive EstimatorsThere is a more efficient estimator for the internal energy calledthe “virial”. Standard Deviation: 0.522(prim); 0.220(vir).
εvir =1
2P
P∑k=1
xk∂V/∂xk +1P
P∑k=1
V (xk) ,
Instantaneous values of virial (orange) and primitive (black)estimators for V (x) = x2/2 at β = 10,P = 64.
0 2e+05 4e+05 6e+05 8e+05 1e+06Time Step (dt=0.01)
-1
-0.5
0
0.5
1
1.5
Tot
al E
nerg
y (n
atur
al u
nits
)
PrimVir
![Page 42: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/42.jpg)
Isotope Effect via Thermodynamic Integration (TI)
Motivation: No PI method to study Isotope Effect (IE).Enzyme catalysis: proton transfer is the rate limiting step in
many enzymatic reactions (dehydrogenases): large IE.Acid dissociation, etc.
Typically, Site–H reacts faster than Site–D.
∆F = F(mf)− F (mi) =
∫ 1
0dλ(
dFdλ
),
where F = − 1β ln Z is the (quantum) free energy.
For a linear path m (λ) = λmf + (1− λ) mi.
![Page 43: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/43.jpg)
Isotope Effect via Thermodynamic Integration (TI)
Motivation: No PI method to study Isotope Effect (IE).Enzyme catalysis: proton transfer is the rate limiting step in
many enzymatic reactions (dehydrogenases): large IE.Acid dissociation, etc.
Typically, Site–H reacts faster than Site–D.
∆F = F(mf)− F (mi) =
∫ 1
0dλ(
dFdλ
),
where F = − 1β ln Z is the (quantum) free energy.
For a linear path m (λ) = λmf + (1− λ) mi.
![Page 44: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/44.jpg)
Isotope Effect via Thermodynamic Integration (TI)
Z(β) ≈n∏
i=1
(miP
2πβ~2
)3P/2 ∫dnPr e−β
∑ni=1∑P
s=1
[mi2 ω
2P(ri,s−ri,s+1)
2+
U(rs)P
].
Two PI estimators for dFdλ :
primitive(dFdλ
)prim
= −N∑
I=1
(m′ImI
)[3P2β−
⟨mI
2ω2
P
P∑s=1
(rI,s − rI,s+1)2
⟩λ
],
and the virial(dFdλ
)vir
= −N∑
I=1
(m′ImI
)[3
2β+
⟨1
2P
P∑s=1
rI,s · ∂rI V (rs)
⟩λ
].
![Page 45: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/45.jpg)
Isotope Effect via Thermodynamic Integration (TI)
Z(β) ≈n∏
i=1
(miP
2πβ~2
)3P/2 ∫dnPr e−β
∑ni=1∑P
s=1
[mi2 ω
2P(ri,s−ri,s+1)
2+
U(rs)P
].
Two PI estimators for dFdλ :
primitive(dFdλ
)prim
= −N∑
I=1
(m′ImI
)[3P2β−
⟨mI
2ω2
P
P∑s=1
(rI,s − rI,s+1)2
⟩λ
],
and the virial(dFdλ
)vir
= −N∑
I=1
(m′ImI
)[3
2β+
⟨1
2P
P∑s=1
rI,s · ∂rI V (rs)
⟩λ
].
![Page 46: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/46.jpg)
Isotope Effect via PIMD
Results for an analytically solvable system (harmonic potential)
0 0.2 0.4 0.6 0.8 1λ
-0.25
-0.2
-0.15
-0.1
dF/d
λ
exactvirprim
0 0.2 0.4 0.6 0.8 1λ
-0.3
-0.2
-0.1
0
dF/d
λ
exact
vir
prim
First derivative of quantum free energy with respect to mass.Left: m (λ) = λmf + (1− λ) mi.Right: m (λ) = λ4mf +
(1− λ4
)mi
Black: exact result. Red: virial and Blue: primitive estimators.
![Page 47: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/47.jpg)
Isotope Effect via TI-PIMDTwo-oscillator model for O− H(D) · · ·O. (Antisymmetric Mode)Useful to compute IE & understand Ubbelohde effect.
0 0.2 0.4 0.6 0.8 1λ
-0.5
-0.4
-0.3
-0.2
-0.1
0dF
/dλ
exactprimvir
100,000 PIMD steps/window: prim=-0.2035, vir=-0.2052,exact=-0.2042.
![Page 48: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/48.jpg)
Simultaneous change in mass and potentialChange of identity/interaction potential: Useful to study Hbinding to active sites.(
dFdλ
)=
~4√
(κ/m)coth
(β~2
√κ/m
)[mκ′ − m′κ
m2
].
0 0.2 0.4 0.6 0.8 1λ
0.1
0.2
0.3
0.4
0.5
dF/d
λ
exact
prim
vir
0 0.2 0.4 0.6 0.8 1λ
0
0.1
0.2
0.3
0.4
dF/d
λ
prim
exact
vir
First derivative of the quantum free energy with respect to mass& force constant for harmonic potential.Left: Linear path. Right: quartic path.Black: primitive result. Red: exact and Blue: virial estimators.
![Page 49: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/49.jpg)
Perturbation TheoryMotivation: PI calculations are expensive!
∆F = − 1β
[3NP
2ln(
mf
mi
)+ ln
⟨e−β(mf−mi)
ω2P
2 A⟩
i
],
where A =∑N
I=1∑P
s=1 (rI,s − rI,s+1)2.Full PT for free energy difference due to isotope transformationusing single PIMD simulation.
100000 200000 300000 400000number PIMD steps (dt=0.01)
-0.22
-0.2
-0.18
-0.16
F(m
=2.
0) -
F(m
=1.
0)
PertExact
0 100000 200000 300000 400000number PIMD steps (dt=0.01)
-0.16
-0.14
-0.12
-0.1
-0.08
-0.06
-0.04
-0.02
0
F(m
=1.
5) -
F(m
=1.
0)
PertExact
Left: mi = 1→ mf = 2. Right: mi = 1→ mf = 1.5.Exact: red horizontal line.PT works provided change is small · · · Multistage-PT.
![Page 50: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/50.jpg)
Perturbation Theory (II)Effect of a static electric field:
∆F = − 1β
ln 〈exp [−β (qE · r)]〉E=0.
Useful to understand ferro/paraelectric hydrogen-bonded solids(KDP), Stark Effect.
0 2e+05 4e+05 6e+05 8e+05 1e+06MD step (dt=0.05)
-0.65
-0.6
-0.55
-0.5
-0.45
F(E
=1)
- F
(E=
0)
ExactPert
-2
-1.75
-1.5
-1.25
F(E
=2)
- F
(E=
0)
ExactPert
![Page 51: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/51.jpg)
λ-dynamics PIMD
Allow λ to vary in a continuous way using single PIMDsimulation.Example: transmutation of diatomics H2 →HCl at 300 K.
0.4
0.5
0.6
0.7
0.8
0.9
1
0 0.2 0.4 0.6 0.8 1
dF/d
λ
λ
numericalexact
∆F = F (HCl)− F (H2) = −0.00332 a.u. (exact), -0.00332 a.u.(numerical).
![Page 52: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/52.jpg)
Isotope effects in the Zundel cation
Important in hydrogen-bonded liquids & in enzymatic reactions.
CPMD Details: Ab initio PIMD (H2 → D2).BLYP/100 Ry, Cubic Box 123 A3, P = 32, T=300 K.
Numerical (PT) ≈ 4 kcal/mol.CPL 329, 36 (2000).
![Page 53: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/53.jpg)
Goal: change of identity in PIMD simulations
Feasible in force fields-PIMD, harder in ab initio PIMD(pseudos).
Example: protonated water/ammonia complexH2O · · · H+ · · · OH2 → H2O · · · H+ · · · NH3
Towards predicting changes in free energy barriers heights?
Predict kinetic isotope effect kH/kD ≈ e−β(
∆F‡H−∆F‡
D
).
![Page 54: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/54.jpg)
![Page 55: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/55.jpg)
Outline
Introduction to Path Integrals
Double proton transfer in DNA base pair models
Development of free energy methods in PIMD
Improving the convergence of PIMD
Summary
![Page 56: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/56.jpg)
Higher-order methods to improve PIMD averages
IDEA Why not to use the classical forces to improve averages?
⟨O⟩≈ 〈O (r1) w (r1, · · · , rP)〉
〈w (r1, · · · , rP)〉.
w (r;β) weighting function constructed using classical forces.In some cases, fourth-order convergence can be attained
without additional overhead!
G. Voth et al, JCP 115, 7832 (2001).A. Perez & M. Tuckerman, JCP (in review).
![Page 57: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/57.jpg)
Higher-order methods to improve PIMD averages
IDEA Why not to use the classical forces to improve averages?
⟨O⟩≈ 〈O (r1) w (r1, · · · , rP)〉
〈w (r1, · · · , rP)〉.
w (r;β) weighting function constructed using classical forces.In some cases, fourth-order convergence can be attained
without additional overhead!
G. Voth et al, JCP 115, 7832 (2001).A. Perez & M. Tuckerman, JCP (in review).
![Page 58: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/58.jpg)
Harmonic potential at β~ω = 10
![Page 59: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/59.jpg)
Hydrogen molecule at 300K: D [1− exp (−a (x− xeq))]
![Page 60: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/60.jpg)
Hydrogen molecule: Ab initio PIMD
Details: T=300K, CPMD BLYP/75 Ry, Cubic Box 93 A3.
![Page 61: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/61.jpg)
High order PIMD methods
Liquid water at ambient temperature (q-SPC/Fw force field1)
P 2nd 4th4 -0.2778 0.59898 0.0400 0.391116 0.2699 0.389232 0.3688 0.405564 0.3968 0.4067
Energy values in a.u.
I Useful to converge faster averages in quantum simulationsof bulk phases.
I Very easy to implement in existing ab initio PIMD codes.I No overhead associated.
1 JCP 125, 184507 (2006).
![Page 62: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/62.jpg)
Outline
Introduction to Path Integrals
Double proton transfer in DNA base pair models
Development of free energy methods in PIMD
Improving the convergence of PIMD
Summary
![Page 63: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/63.jpg)
Summary
I The Feynman’s path integral formalism was reviewed &applied to several systems
I Nuclear quantum effects are important even at roomtemperature
I “Rare” tautomers dynamically unstable & not implicated inmutations
I New estimators were derived & implemented to investigatealchemical transformations
I Higher-order algorithm to improve convergence of PIMDestimators
![Page 64: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/64.jpg)
Acknowledgments
The beautiful town of Baiona
Thanks for your attention! Questions?
![Page 65: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/65.jpg)
Acknowledgments
The beautiful town of Baiona
Thanks for your attention! Questions?
![Page 66: PATH INTEGRAL MOLECULAR DYNAMICS ...helper.ipam.ucla.edu/publications/ccsws4/ccsws4_9912.pdfPATH INTEGRAL MOLECULAR DYNAMICS: APPLICATIONS & NEW ALGORITHMS. Alejandro Perez Paz´ Nano-bio](https://reader030.vdocuments.net/reader030/viewer/2022040510/5e59e4578228100bf60021b5/html5/thumbnails/66.jpg)
Acknowledgments
The beautiful town of Baiona
Thanks for your attention! Questions?