%0 Journal Article %1 ISI:000258490600008 %A Pan, Albert C. %A Roux, Benoit %C CIRCULATION & FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA %D 2008 %I AMER INST PHYSICS %J JOURNAL OF CHEMICAL PHYSICS %K energies free markov model pathways rates state transition %N 6 %R 10.1063/1.2959573 %T Building Markov state models along pathways to determine free energies and rates of transitions %V 129 %X An efficient method is proposed for building Markov models with discrete states able to accurately describe the slow relaxation of a complex system with two stable conformations. First, the reaction pathway described by a set of collective variables between the two stable states is determined using the string method with swarms of trajectories. Then, short trajectories are initiated at different points along this pathway to build the state-to-state transition probability matrix. It is shown, using a model system, how this strategy makes it possible to use trajectories that are significantly shorter than the slowest relaxation time to efficiently build a reliable and accurate Markov model. Extensions of the method to multiple pathways, as well as some common pitfalls arising from poorly relaxed paths or an inappropriate choice of collective variables, are illustrated and discussed. (C) 2008 American Institute of Physics.

@article{ISI:000258490600008, abstract = {{An efficient method is proposed for building Markov models with discrete states able to accurately describe the slow relaxation of a complex system with two stable conformations. First, the reaction pathway described by a set of collective variables between the two stable states is determined using the string method with swarms of trajectories. Then, short trajectories are initiated at different points along this pathway to build the state-to-state transition probability matrix. It is shown, using a model system, how this strategy makes it possible to use trajectories that are significantly shorter than the slowest relaxation time to efficiently build a reliable and accurate Markov model. Extensions of the method to multiple pathways, as well as some common pitfalls arising from poorly relaxed paths or an inappropriate choice of collective variables, are illustrated and discussed. (C) 2008 American Institute of Physics.}}, added-at = {2009-01-04T01:49:16.000+0100}, address = {{CIRCULATION \& FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA}}, affiliation = {{Pan, AC (Reprint Author), Univ Chicago, Dept Biochem \& Mol Biol, Gordon Ctr Integrat Sci, 920 E 58Th St, Chicago, IL 60637 USA. {[}Pan, Albert C.; Roux, Benoit] Univ Chicago, Dept Biochem \& Mol Biol, Gordon Ctr Integrat Sci, Chicago, IL 60637 USA. {[}Roux, Benoit] Argonne Natl Lab, Div Math \& Comp Sci, Biosci Div, Argonne, IL 60439 USA.}}, article-number = {{064107}}, author = {Pan, Albert C. and Roux, Benoit}, author-email = {{roux@uchicago.edu}}, biburl = {https://www.bibsonomy.org/bibtex/2493933e7b39943ed0c86fb639431a254/huiyangsfsu}, cited-references = {{ALLEN MP, 1987, COMPUTER SIMULATION. BOLHUIS PG, 2002, ANNU REV PHYS CHEM, V53, P291. BROOKS BR, 1983, J COMPUT CHEM, V4, P187. BUCHETE V, 2008, PHYS REV E, V77, UNSP 030902. CHANDLER D, 1978, J CHEM PHYS, V68, P2959. CHODERA JD, 2006, MULTISCALE MODEL SIM, V5, P1214, DOI 10.1137/06065146X. CHODERA JD, 2007, J CHEM PHYS, V126, ARTN 155101. DU R, 1998, J CHEM PHYS, V108, P334. ELMER SP, 2005, J CHEM PHYS, V123, ARTN 114902. ELMER SP, 2005, J CHEM PHYS, V123, ARTN 114903. FARADJIAN AK, 2004, J CHEM PHYS, V120, P10880, DOI 10.1063/1.1738640. GALASSI M, 2006, GNU SCI LIB REFERENC. GEISSLER PL, 1999, J PHYS CHEM B, V103, P3706. HILLE B, 2001, ION CHANNELS EXCITAB. HINRICHS NS, 2007, J CHEM PHYS, V126, ARTN 244101. HUMMER G, 2003, J CHEM PHYS, V118, P10762, DOI 10.1063/1.1574777. JAYACHANDRAN G, 2006, J CHEM PHYS, V124, P64902. KASSON PM, 2007, PLOS COMPUT BIOL, V3, P2228, ARTN e220. MARAGLIANO L, 2006, J CHEM PHYS, V125, ARTN 024106. MORONI D, 2004, J CHEM PHYS, V120, P4055, DOI 10.1063/1.1644537. PAN AC, 2008, J PHYS CHEM B, V112, P3432, DOI 10.1021/jp0777059. PARK S, 2007, BIOPHYS J, V93, P4108, DOI 10.1529/biophysj.107.108100. REN W, 2005, J CHEM PHYS, V123, ARTN 134109. REN WEW, 2002, PHYS REV B, V66, UNSP 052301. SEZER D, 2008, J PHYS CHEM B, V112, P5755, DOI 10.1021/jp711375x. SINGHAL N, 2004, J CHEM PHYS, V121, P415, DOI 10.1063/1.1738647. SINGHAL N, 2005, J CHEM PHYS, V123, ARTN 204909. SRIRAMAN S, 2005, J PHYS CHEM B, V109, P6479, DOI 10.1021/jp046448u. SWOPE WC, 2004, J PHYS CHEM B, V108, P6571, DOI 10.1021/jp037421y. SWOPE WC, 2004, J PHYS CHEM B, V108, P6582, DOI 10.1021/jp037422q. VANDENEIJNDEN E, 2006, TRANSITION PATH THEO, V2, P439. VANERP TS, 2003, J CHEM PHYS, V118, P7762, DOI 10.1063/1.1562614. VOLKMAN BF, 2001, SCIENCE, V291, P2429. VOTER AF, 1998, PHYS REV B, V57, UNSP R13985. WEINAN E, 2005, J PHYS CHEM B, V109, P6688, DOI 10.1021/jp0455430.}}, doc-delivery-number = {{338FD}}, doi = {{10.1063/1.2959573}}, interhash = {4bbf8e60e55c08afba78ff213437d414}, intrahash = {493933e7b39943ed0c86fb639431a254}, issn = {{0021-9606}}, journal = {{JOURNAL OF CHEMICAL PHYSICS}}, journal-iso = {{J. Chem. Phys.}}, keywords = {energies free markov model pathways rates state transition}, keywords-plus = {{MOLECULAR-DYNAMICS SIMULATIONS; PROTEIN-FOLDING KINETICS; RATE CONSTANTS; STRING METHOD; BETA-HAIRPIN; PEPTIDE; EVENTS; HELIX}}, language = {{English}}, month = {{AUG 14}}, number = {{6}}, number-of-cited-references = {{35}}, publisher = {{AMER INST PHYSICS}}, subject-category = {{Physics, Atomic, Molecular \& Chemical}}, times-cited = {{0}}, timestamp = {2009-01-04T01:49:16.000+0100}, title = {{Building Markov state models along pathways to determine free energies and rates of transitions}}, type = {{Article}}, unique-id = {{ISI:000258490600008}}, volume = {{129}}, year = {{2008}} }