1 nonlinear instability in multiple time stepping molecular dynamics jesús izaguirre, qun ma,...
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![Page 1: 1 Nonlinear Instability in Multiple Time Stepping Molecular Dynamics Jesús Izaguirre, Qun Ma, Department of Computer Science and Engineering University](https://reader035.vdocuments.us/reader035/viewer/2022062715/56649d6d5503460f94a4cdaf/html5/thumbnails/1.jpg)
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Nonlinear Instability in Multiple Time Stepping Molecular Dynamics
Jesús Izaguirre, Qun Ma, Department of Computer Science and Engineering
University of Notre Dameand
Robert SkeelDepartment of Computer Science and Beckman Institute
University of Illinois, Urbana-Champaign
SAC’03March 10, 2003
Supported by NSF CAREER and BIOCOMPLEXITY grants
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Overview Background
Classical molecular dynamics (MD) Multiple time stepping integrator Linear instability
Nonlinear instabilities Analytical approach Numerical approach Concluding remarks
Acknowledgements Key references
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Overview Background
Classical molecular dynamics (MD) Multiple time stepping integrator Linear instability
Nonlinear instabilities Analytical approach Numerical approach Concluding remarks
Acknowledgements Key references
![Page 4: 1 Nonlinear Instability in Multiple Time Stepping Molecular Dynamics Jesús Izaguirre, Qun Ma, Department of Computer Science and Engineering University](https://reader035.vdocuments.us/reader035/viewer/2022062715/56649d6d5503460f94a4cdaf/html5/thumbnails/4.jpg)
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Classical molecular dynamics Newton’s equations
of motion:
Atoms Molecules CHARMM potential
(Chemistry at Harvard Molecular Mechanics)
'' ( ) ( ). - - - (1)U Mr r F r
Bonds, angles and torsions
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The CHARMM potential terms
Bond Angle
Dihedral Improper
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Energy functions
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Overview Background
Classical molecular dynamics (MD) Multiple time stepping integrator Linear instability
Nonlinear instabilities Analytical approach Numerical approach Concluding remarks
Acknowledgements Key references
![Page 8: 1 Nonlinear Instability in Multiple Time Stepping Molecular Dynamics Jesús Izaguirre, Qun Ma, Department of Computer Science and Engineering University](https://reader035.vdocuments.us/reader035/viewer/2022062715/56649d6d5503460f94a4cdaf/html5/thumbnails/8.jpg)
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Multiple time stepping Fast/slow force splitting
Bonded: “fast” (small periods) Long range nonbonded: “slow” (large char. time)
Evaluate slow forces less frequently
Fast forces cheap Slow force evaluation expensive
Fast forces, t
Slow forces, t
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Verlet-I/r-RESPA/ImpulseGrubmüller,Heller, Windemuth and Schulten, 1991 Tuckerman, Berne and Martyna, 1992
The state-of-the-art MTS integrator Fast/slow splitting of nonbonded terms via switching
functions 2nd order accurate, time reversible
slow1/ 2half kick: ( ) / 2
oscillate: update positions and momentum
using Verlet/leapfrog ( /2, much smaller time steps)
n n nv v t f r
t
Algorithm 1. Half step discretization of Impulse integrator
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Overview Background
Classical molecular dynamics (MD) Multiple time stepping integrator Linear instability
Nonlinear instabilities Analytical approach Numerical approach Concluding remarks
Acknowledgements Key references
![Page 11: 1 Nonlinear Instability in Multiple Time Stepping Molecular Dynamics Jesús Izaguirre, Qun Ma, Department of Computer Science and Engineering University](https://reader035.vdocuments.us/reader035/viewer/2022062715/56649d6d5503460f94a4cdaf/html5/thumbnails/11.jpg)
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Linear instability of Impulse
Total energy(Kcal/mol) vs. time (fs)
Linear instability: energy growth occurs unless longest t < 1/2 shortest period.
Impulse
MOLLY - ShortAvg
MOLLY - LongAvg
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Overview Background
Classical molecular dynamics (MD) Multiple time stepping integrator Linear instability
Nonlinear “instabilities” (overheating) Analytical approach Numerical approach Concluding remarks
Acknowledgements Key references
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Nonlinear instability of Impulse
Approach Analytical: Stability conditions for a nonlinear model
problem Numerical: Long simulations differing only in outer
time steps; correlation between step size and overheating
Results: energy growth occurs unless longest t < 1/3 shortest period.
Unconditionally unstable 3rd order nonlinear resonance Flexible waters: outer time step less than 3~3.3fs Constrained-bond proteins w/ SHAKE: time step less
than 4~5fs
Ma, Izaguirre and Skeel (SISC, 2003)
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Overview Background
Classical molecular dynamics (MD) Multiple time stepping integrator Linear instability
Nonlinear instabilities Analytical approach Numerical approach Concluding remarks
Acknowledgements Key references
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Nonlinear instability: analytical Approach:
1-D nonlinear model problem, in the neighborhood of stable equilibrium
MTS splitting of potential:
Analyze the reversible symplectic map Express stability condition in terms of problem
parameters Result:
3rd order resonance stable only if “equality” met 4th order resonance stable only if “inequality” met Impulse unstable at 3rd order resonance in practice
2 2 2 3 4 5oscillate kick( ) ( / 2) ( / 2 / 3 / 4) ( ).U q q Aq Bq Cq O q
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Nonlinear: analytical (cont.) Main result. Let
1. (3rd order) Map stable at equilibrium if and unstable if
Impulse is unstable in practice. 2. (4th order) Map stable if
and unstable if
May be stable at the 4th order resonance.
2 , where , where
1 ' /(2 ') if ' 0, 0 if ' 0, and
1 ' /(2 ') if s '/ 0, 0 if s '/ 0, and
' sin( / 2) and c ' cos( / 2).
i
hs A c c c
hc A s
s h h
0, 0,B C 0.B
20 or 2 ' '/ ,C C hB s c 20 2 ' '/ .C hB s c
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Overview Background
Classical molecular dynamics (MD) Multiple time stepping integrator Linear instability
Nonlinear instabilities Analytical approach Numerical approach Concluding remarks
Acknowledgements Key references
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Nonlinear resonance: numerical
Fig. 1: Left: Flexible water system. Right: Energy drift from 500ps MD simulation of flexible water at room temperature revealing 3:1 and 4:1 nonlinear resonance (3.3363 and 2.4 fs)
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Nonlinear resonance: numerical
Fig. 2. Energy drift from 500ps MD simulation of flexible water at room temperature revealing 3:1 (3.3363)
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Fig. 3. Left: Flexible melittin protein (PDB entry 2mlt). Right: energy drift from 10ns MD simulation at 300K revealing 3:1 nonlinear resonance (at 3, 3.27 and 3.78 fs).
Nonlinear: numerical (cont.)
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Overview Background
Classical molecular dynamics (MD) Multiple time stepping integrator Linear instability
Nonlinear instabilities Analytical approach Numerical approach Concluding remarks
Acknowledgements Key references
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Concluding remarks MTS restricted by a 3:1 nonlinear
resonance that causes overheating Longest time step < 1/3 fastest normal mode
Important for long MD simulations due to: Faster computers enabling longer simulations Long time kinetics and sampling, e.g., protein
folding Use stochasticity for long time kinetics
For large system size, NVE NVT
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Overview Background
Classical molecular dynamics (MD) Multiple time stepping integrator Linear instability
Nonlinear instabilities Analytical approach Numerical approach Concluding remarks
Acknowledgements Key references
![Page 24: 1 Nonlinear Instability in Multiple Time Stepping Molecular Dynamics Jesús Izaguirre, Qun Ma, Department of Computer Science and Engineering University](https://reader035.vdocuments.us/reader035/viewer/2022062715/56649d6d5503460f94a4cdaf/html5/thumbnails/24.jpg)
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Acknowledgements People
Dr. Thierry Matthey Dr. Ruhong Zhou, Dr. Pierro Procacci Dr. Andrew McCammon hosted JI in May 2001 at
UCSD Dept. of Mathematics, UCSD, hosted RS Aug. 2000 –
Aug. 2001 Resources
Hydra and BOB clusters at ND Norwegian Supercomputing Center, Bergen, Norway
Funding NSF CAREER Award ACI-0135195 NSF BIOCOMPLEXITY-IBN-0083653
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Key references[1] Overcoming instabilities in Verlet-I/r-RESPA with the mollified impulse
method. J. A. Izaguirre, Q. Ma, T. Matthey, et al.. In T. Schlick and H. H. Gan, editors, Proceedings of the 3rd International Workshop on Algorithms for Macromolecular Modeling, Vol. 24 of Lecture Notes in Computational Science and Engineering, pages 146-174, Springer-Verlag, Berlin, New York, 2002
[2] Verlet-I/r-RESPA/Impulse is limited by nonlinear instability. Q. Ma, J. A. Izaguirre, and R. D. Skeel. Accepted by the SIAM Journal on Scientific Computing, 2002. Available at http://www.nd.edu/~qma1/publication_h.html.
[3] Targeted mollified impulse – a multiscale stochastic integrator for molecular dynamics. Q. Ma and J. A. Izaguirre. Submitted to the SIAM Journal on Multiscale Modeling and Simulation, 2003.
[4] Nonlinear instability in multiple time stepping molecular dynamics. Q. Ma, J. A. Izaguirre, and R. D. Skeel. In Proceedings of the 2003 ACM Symposium on Applied Computing (SAC’03), pages 167-171, Melborne, Florida. March 9-12, 2003
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Key references
[5] Long time step molecular dynamics using targeted Langevin Stabilization. Q. Ma and J. A. Izaguirre. In Proceedings of the 2003 ACM Symposium on Applied Computing (SAC’03), pages 178-182, Melborne, Florida. March 9-12, 2003
[6] Dangers of multiple-time-step methods. J. J. Biesiadecki and R. D. Skeel. J. Comp. Phys., 109(2):318–328, Dec. 1993.
[7] Difficulties with multiple time stepping and the fast multipole algorithm in molecular dynamics. T. Bishop, R. D. Skeel, and K. Schulten. J. Comp. Chem., 18(14):1785–1791, Nov. 15, 1997.
[8] Masking resonance artifacts in force-splitting methods for biomolecular simulations by extrapolative Langevin dynamics. A. Sandu and T. Schlick. J. Comut. Phys, 151(1):74-113, May 1, 1999
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THE END. THANKS!
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Nonlinear: numerical (cont.)
Fig. 4. Left: Melittin protein and water. Right: Energy drift from 500ps SHAKE- constrained MD simulation at 300K revealing combined 4:1 and 3:1 nonlinear resonance.