Adaptive ensemble simulations of biomolecules

Kasson, Peter M.; Jha, Shantenu

doi:10.1016/j.sbi.2018.09.005

Title: Adaptive ensemble simulations of biomolecules

Journal Article · 24 September 2018 · Current Opinion in Structural Biology

DOI: https://doi.org/10.1016/j.sbi.2018.09.005 · OSTI ID:1491694

Kasson, Peter M. ^[1]; Jha, Shantenu ^[2]

Univ. of Virginia, Charlottesville, VA (United States); Uppsala Univ., Uppsala (Sweden)
Rutgers Univ., Piscataway, NJ (United States); Brookhaven National Lab. (BNL), Upton, NY (United States)

Recent advances in both theory and computational power have created opportunities to simulate biomolecular processes more efficiently using adaptive ensemble simulations. Ensemble simulations are now widely used to compute a number of individual simulation trajectories and analyze statistics across them. Adaptive ensemble simulations offer a further level of sophistication and flexibility by enabling highlevel algorithms to control simulations-based on intermediate results. We review some of the adaptive ensemble algorithms and software infrastructure currently in use and outline where the complexities of implementing adaptive simulation have limited algorithmic innovation to date. In conclusion, we describe an adaptive ensemble API to overcome some of these barriers and more flexibly and simply express adaptive simulation algorithms to help realize the power of this type of simulation.

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Research Organization:: Brookhaven National Laboratory (BNL), Upton, NY (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Advanced Scientific Computing Research (SC-21)

Grant/Contract Number:: SC0012704

OSTI ID:: 1491694

Report Number(s):: BNL--210893-2019-JAAM

Journal Information:: Current Opinion in Structural Biology, Journal Name: Current Opinion in Structural Biology Journal Issue: C Vol. 52; ISSN 0959-440X

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

References (51)

Multidimensional adaptive umbrella sampling: Applications to main chain and side chain peptide conformations Bartels, Christian; Karplus, Martin Journal of Computational Chemistry, Vol. 18, Issue 12 https://doi.org/10.1002/(SICI)1096-987X(199709)18:12<1450::AID-JCC3>3.0.CO;2-I	journal	September 1997
Extracting macroscopic stochastic dynamics: Model problems: Extracting Macroscopic Dynamics Huisinga, Wilhelm; Schütte, Christof; Stuart, Andrew M. Communications on Pure and Applied Mathematics, Vol. 56, Issue 2 https://doi.org/10.1002/cpa.10057	journal	November 2002
FireWorks: a dynamic workflow system designed for high-throughput applications: FireWorks: A Dynamic Workflow System Designed for High-Throughput Applications Jain, Anubhav; Ong, Shyue Ping; Chen, Wei Concurrency and Computation: Practice and Experience, Vol. 27, Issue 17 https://doi.org/10.1002/cpe.3505	journal	May 2015
Improving the efficiency and reliability of free energy perturbation calculations using overlap sampling methods Lu, Nandou; Kofke, David A.; Woolf, Thomas B. Journal of Computational Chemistry, Vol. 25, Issue 1 https://doi.org/10.1002/jcc.10369	journal	January 2003
Scalable molecular dynamics with NAMD Phillips, James C.; Braun, Rosemary; Wang, Wei Journal of Computational Chemistry, Vol. 26, Issue 16, p. 1781-1802 https://doi.org/10.1002/jcc.20289	journal	January 2005
The Amber biomolecular simulation programs Case, David A.; Cheatham, Thomas E.; Darden, Tom Journal of Computational Chemistry, Vol. 26, Issue 16 https://doi.org/10.1002/jcc.20290	journal	January 2005
CHARMM: The biomolecular simulation program Brooks, B. R.; Brooks, C. L.; Mackerell, A. D. Journal of Computational Chemistry, Vol. 30, Issue 10 https://doi.org/10.1002/jcc.21287	journal	July 2009
Parallel tempering algorithm for conformational studies of biological molecules Hansmann, Ulrich H. E. Chemical Physics Letters, Vol. 281, Issue 1-3 https://doi.org/10.1016/S0009-2614(97)01198-6	journal	December 1997
Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC) Galindo-Murillo, Rodrigo; Roe, Daniel R.; Cheatham, Thomas E. Biochimica et Biophysica Acta (BBA) - General Subjects, Vol. 1850, Issue 5 https://doi.org/10.1016/j.bbagen.2014.09.007	journal	May 2015
The parallel replica dynamics method – Coming of age Perez, Danny; Uberuaga, Blas P.; Voter, Arthur F. Computational Materials Science, Vol. 100 https://doi.org/10.1016/j.commatsci.2014.12.011	journal	April 2015
PLUMED: A portable plugin for free-energy calculations with molecular dynamics Bonomi, Massimiliano; Branduardi, Davide; Bussi, Giovanni Computer Physics Communications, Vol. 180, Issue 10 https://doi.org/10.1016/j.cpc.2009.05.011	journal	October 2009
PLUMED 2: New feathers for an old bird Tribello, Gareth A.; Bonomi, Massimiliano; Branduardi, Davide Computer Physics Communications, Vol. 185, Issue 2 https://doi.org/10.1016/j.cpc.2013.09.018	journal	February 2014
Dynamic steering of HPC scientific workflows: A survey Mattoso, Marta; Dias, Jonas; Ocaña, Kary A. C. S. Future Generation Computer Systems, Vol. 46 https://doi.org/10.1016/j.future.2014.11.017	journal	May 2015
Generalized-ensemble algorithms: enhanced sampling techniques for Monte Carlo and molecular dynamics simulations Okamoto, Yuko Journal of Molecular Graphics and Modelling, Vol. 22, Issue 5 https://doi.org/10.1016/j.jmgm.2003.12.009	journal	May 2004
Swift: A language for distributed parallel scripting Wilde, Michael; Hategan, Mihael; Wozniak, Justin M. Parallel Computing, Vol. 37, Issue 9 https://doi.org/10.1016/j.parco.2011.05.005	journal	September 2011
Molecular Simulation Workflows as Parallel Algorithms: The Execution Engine of Copernicus, a Distributed High-Performance Computing Platform Pronk, Sander; Pouya, Iman; Lundborg, Magnus Journal of Chemical Theory and Computation, Vol. 11, Issue 6 https://doi.org/10.1021/acs.jctc.5b00234	journal	May 2015
Rapid Computation of Thermodynamic Properties over Multidimensional Nonbonded Parameter Spaces Using Adaptive Multistate Reweighting Naden, Levi N.; Shirts, Michael R. Journal of Chemical Theory and Computation, Vol. 12, Issue 4 https://doi.org/10.1021/acs.jctc.5b00869	journal	February 2016
Leveraging the Information from Markov State Models To Improve the Convergence of Umbrella Sampling Simulations Jo, Sunhwan; Suh, Donghyuk; He, Ziwei The Journal of Physical Chemistry B, Vol. 120, Issue 33 https://doi.org/10.1021/acs.jpcb.6b05125	journal	May 2016
Conformational Intermediate That Controls KPC-2 Catalysis and Beta-Lactam Drug Resistance Cortina, George A.; Hays, Jennifer M.; Kasson, Peter M. ACS Catalysis, Vol. 8, Issue 4 https://doi.org/10.1021/acscatal.7b03832	journal	February 2018
Accurate Ensemble Molecular Dynamics Binding Free Energy Ranking of Multidrug-Resistant HIV-1 Proteases Sadiq, S. Kashif; Wright, David W.; Kenway, Owain A. Journal of Chemical Information and Modeling, Vol. 50, Issue 5 https://doi.org/10.1021/ci100007w	journal	April 2010
WESTPA: An Interoperable, Highly Scalable Software Package for Weighted Ensemble Simulation and Analysis Zwier, Matthew C.; Adelman, Joshua L.; Kaus, Joseph W. Journal of Chemical Theory and Computation, Vol. 11, Issue 2 https://doi.org/10.1021/ct5010615	journal	January 2015
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation Hess, Berk; Kutzner, Carsten; van der Spoel, David Journal of Chemical Theory and Computation, Vol. 4, Issue 3 https://doi.org/10.1021/ct700301q	journal	February 2008
Enhanced Modeling via Network Theory: Adaptive Sampling of Markov State Models Bowman, Gregory R.; Ensign, Daniel L.; Pande, Vijay S. Journal of Chemical Theory and Computation, Vol. 6, Issue 3 https://doi.org/10.1021/ct900620b	journal	February 2010
Mapping Long-Range Interactions in α-Synuclein using Spin-Label NMR and Ensemble Molecular Dynamics Simulations Dedmon, Matthew M.; Lindorff-Larsen, Kresten; Christodoulou, John Journal of the American Chemical Society, Vol. 127, Issue 2 https://doi.org/10.1021/ja044834j	journal	January 2005
Water Ordering at Membrane Interfaces Controls Fusion Dynamics Kasson, Peter M.; Lindahl, Erik; Pande, Vijay S. Journal of the American Chemical Society, Vol. 133, Issue 11 https://doi.org/10.1021/ja200310d	journal	March 2011
Describing Protein Folding Kinetics by Molecular Dynamics Simulations. 1. Theory ^† Swope, William C.; Pitera, Jed W.; Suits, Frank The Journal of Physical Chemistry B, Vol. 108, Issue 21 https://doi.org/10.1021/jp037421y	journal	May 2004
Efficient Reconstruction of Complex Free Energy Landscapes by Multiple Walkers Metadynamics ^† Raiteri, Paolo; Laio, Alessandro; Gervasio, Francesco Luigi The Journal of Physical Chemistry B, Vol. 110, Issue 8 https://doi.org/10.1021/jp054359r	journal	March 2006
Finding Transition Pathways Using the String Method with Swarms of Trajectories Pan, Albert C.; Sezer, Deniz; Roux, Benoît The Journal of Physical Chemistry B, Vol. 112, Issue 11 https://doi.org/10.1021/jp0777059	journal	March 2008
Complete protein–protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling Plattner, Nuria; Doerr, Stefan; De Fabritiis, Gianni Nature Chemistry, Vol. 9, Issue 10 https://doi.org/10.1038/nchem.2785	journal	June 2017
Predicting allosteric mutants that increase activity of a major antibiotic resistance enzyme Latallo, M. J.; Cortina, G. A.; Faham, S. Chemical Science, Vol. 8, Issue 9 https://doi.org/10.1039/C7SC02676E	journal	January 2017
Determination of solvation free energies by adaptive expanded ensemble molecular dynamics Åberg, K. Magnus; Lyubartsev, Alexander P.; Jacobsson, Sven P. The Journal of Chemical Physics, Vol. 120, Issue 8 https://doi.org/10.1063/1.1642601	journal	February 2004
Computing time scales from reaction coordinates by milestoning Faradjian, Anton K.; Elber, Ron The Journal of Chemical Physics, Vol. 120, Issue 23 https://doi.org/10.1063/1.1738640	journal	June 2004
Calculation of the distribution of eigenvalues and eigenvectors in Markovian state models for molecular dynamics Hinrichs, Nina Singhal; Pande, Vijay S. The Journal of Chemical Physics, Vol. 126, Issue 24 https://doi.org/10.1063/1.2740261	journal	June 2007
Adaptively biased molecular dynamics for free energy calculations Babin, Volodymyr; Roland, Christopher; Sagui, Celeste The Journal of Chemical Physics, Vol. 128, Issue 13 https://doi.org/10.1063/1.2844595	journal	April 2008
Markovian milestoning with Voronoi tessellations Vanden-Eijnden, Eric; Venturoli, Maddalena The Journal of Chemical Physics, Vol. 130, Issue 19 https://doi.org/10.1063/1.3129843	journal	May 2009
Markov models of molecular kinetics: Generation and validation Prinz, Jan-Hendrik; Wu, Hao; Sarich, Marco The Journal of Chemical Physics, Vol. 134, Issue 17 https://doi.org/10.1063/1.3565032	journal	May 2011
New approach to Monte Carlo calculation of the free energy: Method of expanded ensembles Lyubartsev, A. P.; Martsinovski, A. A.; Shevkunov, S. V. The Journal of Chemical Physics, Vol. 96, Issue 3 https://doi.org/10.1063/1.462133	journal	February 1992
Efficiently sampling conformations and pathways using the concurrent adaptive sampling (CAS) algorithm Ahn, Surl-Hee; Grate, Jay W.; Darve, Eric F. The Journal of Chemical Physics, Vol. 147, Issue 7 https://doi.org/10.1063/1.4999097	journal	August 2017
Ensemble molecular dynamics yields submillisecond kinetics and intermediates of membrane fusion Kasson, P. M.; Kelley, N. W.; Singhal, N. Proceedings of the National Academy of Sciences, Vol. 103, Issue 32 https://doi.org/10.1073/pnas.0601597103	journal	July 2006
Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations Noé, Frank; Schütte, Christof; Vanden-Eijnden, Eric Proceedings of the National Academy of Sciences, Vol. 106, Issue 45 https://doi.org/10.1073/pnas.0905466106	journal	November 2009
GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit Pronk, Sander; Páll, Szilárd; Schulz, Roland Bioinformatics, Vol. 29, Issue 7 https://doi.org/10.1093/bioinformatics/btt055	journal	February 2013
gmxapi: a high-level interface for advanced control and extension of molecular dynamics simulations Irrgang, M. Eric; Hays, Jennifer M.; Kasson, Peter M. Bioinformatics, Vol. 34, Issue 22 https://doi.org/10.1093/bioinformatics/bty484	journal	June 2018
The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud Wolstencroft, Katherine; Haines, Robert; Fellows, Donal Nucleic Acids Research, Vol. 41, Issue W1 https://doi.org/10.1093/nar/gkt328	journal	May 2013
Replica Monte Carlo Simulation of Spin-Glasses Swendsen, Robert H.; Wang, Jian-Sheng Physical Review Letters, Vol. 57, Issue 21 https://doi.org/10.1103/PhysRevLett.57.2607	journal	November 1986
Science in the Cloud: Accelerating Discovery in the 21st Century Hellerstein, Joseph L.; Kohlhoff, Kai J.; Konerding, David E. IEEE Internet Computing, Vol. 16, Issue 4 https://doi.org/10.1109/MIC.2012.87	journal	July 2012
COMPUTING: Screen Savers of the World Unite! Shirts, M. Science, Vol. 290, Issue 5498 https://doi.org/10.1126/science.290.5498.1903	journal	December 2000
Long‐Time Protein Folding Dynamics from Short‐Time Molecular Dynamics Simulations Chodera, John D.; Swope, William C.; Pitera, Jed W. Multiscale Modeling & Simulation, Vol. 5, Issue 4 https://doi.org/10.1137/06065146X	journal	January 2006
Extended Ensemble Monte Carlo Iba, Yukito International Journal of Modern Physics C, Vol. 12, Issue 05 https://doi.org/10.1142/S0129183101001912	journal	June 2001
Exchange Monte Carlo Method and Application to Spin Glass Simulations Hukushima, Koji; Nemoto, Koji Journal of the Physical Society of Japan, Vol. 65, Issue 6 https://doi.org/10.1143/JPSJ.65.1604	journal	June 1996
MapReduce: simplified data processing on large clusters Dean, Jeffrey; Ghemawat, Sanjay; Mehta, Brijesh Communications of the ACM, Vol. 51, Issue 1 https://doi.org/10.1145/1327452.1327492	journal	January 2008
Atomic-Resolution Simulations Predict a Transition State for Vesicle Fusion Defined by Contact of a Few Lipid Tails Kasson, Peter M.; Lindahl, Erik; Pande, Vijay S. PLoS Computational Biology, Vol. 6, Issue 6 https://doi.org/10.1371/journal.pcbi.1000829	journal	June 2010

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