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Analysis of the accelerated weighted ensemble methodology
1. | Mechanical Engineering Department, Stanford University, CA, United States |
2. | Computer Science and Engineering, University of Notre Dame, IN, United States, United States |
3. | Mechanical Engineering Department and Institute for Computational and Mathematical Engineering, Stanford University, CA, United States |
References:
[1] |
D. Bhatt and D. M. Zuckerman, Heterogeneous path ensembles for conformational transitions in semiatomistic models of adenylate kinase, Journal of Chemical Theory and Computation, 6 (2010), 3527-3539. |
[2] |
D. Bhatt, B. W. Zhang, and D. M. Zuckerman, Steady-state simulations using weighted ensemble path sampling, The Journal of Chemical Physics, 133 (2010), 014110. |
[3] |
D. Bhatt and D. M. Zuckerman, Symmetry of forward and reverse path populations, arXiv:1002.2402 (physics.comp-ph), 2010. |
[4] |
E. Darve and E. Ryu, Computing reaction rates in bio-molecular systems using discrete macro-states, Innovations in Biomolecular Modeling and Simulations,1 (2012), 138-206. |
[5] |
A. Dickson and A. R. Dinner., Enhanced Sampling of Nonequilibrium Steady States, Annu. Rev. Phys. Chem., 61 (2010), 441-459. |
[6] |
A. Dickson, A. Warmflash and A. R. Dinner., Separating forward and backward pathways in nonequilibrium umbrella sampling, J. Chem. Phys., 131 (2009), 154104. |
[7] |
A. Dickson, A. Warmflash and A. R. Dinner., Nonequilibrium umbrella sampling in spaces of many order parameters, J. Chem. Phys., 130 (2009), 074104. |
[8] |
W. E and E. Vanden-Eijnden, Towards a Theory of Transition Paths, Journal of Statistical Physics, 123 (2006), 503-523. |
[9] |
G. A. Huber and S. Kim, Weighted ensemble Brownian dynamics simulations for protein association reactions, Biophysical journal, 70 (1996), 97110. |
[10] |
P. Metzner, C. Schütte and E. Vanden-Eijnden, Illustration of transition path theory on a collection of simple examples, The Journal of Chemical Physics, 125 (2006), 084110. |
[11] |
V. S. Pande, K. Beauchamp and G. R. Bowman, Everything you wanted to know about Markov state models but were afraid to ask, Methods, 52 (2010), 99105. |
[12] |
N. Singhal and V. S. Pande, Error analysis and efficient sampling in Markovian state models for molecular dynamics, The Journal of Chemical Physics, 123 (2005), 204909. |
[13] |
W. C. Swope, J. W. Pitera and F. Suits, Describing Protein Folding Kinetics by Molecular Dynamics Simulations. 1. Theory, The Journal of Physical Chemistry B, 108 (2004), 65716581. |
[14] |
E. Vanden-Eijnden, M. Venturoli, G. Ciccotti and R. Elber, On the assumptions underlying milestoning, The Journal of Chemical Physics, 129 (2008), 174102. |
[15] |
E. Vanden-Eijnden and M. Venturoli., Exact rate calculations by trajectory parallelization and tilting, J. Chem. Phys., 131 (2009), 044120. |
[16] |
A. Warmflash, P. Bhimalapuram and A. R. Dinner., Umbrella sampling for nonequilibrium processes, J. Chem. Phys., 127 (2007), 154112. |
[17] |
B. W Zhang, D. Jasnow and D. M. Zuckerman, "Weighted Ensemble Path Sampling for Multiple Reaction Channels," arXiv.org, physics.bio-ph, February 2009. |
[18] |
B. W. Zhang, D. Jasnow and D. M. Zuckerman, The "weighted ensemble" path sampling method is statistically exact for a broad class of stochastic processes and binning procedures, The Journal of Chemical Physics, 132 (2010), 054107. |
show all references
References:
[1] |
D. Bhatt and D. M. Zuckerman, Heterogeneous path ensembles for conformational transitions in semiatomistic models of adenylate kinase, Journal of Chemical Theory and Computation, 6 (2010), 3527-3539. |
[2] |
D. Bhatt, B. W. Zhang, and D. M. Zuckerman, Steady-state simulations using weighted ensemble path sampling, The Journal of Chemical Physics, 133 (2010), 014110. |
[3] |
D. Bhatt and D. M. Zuckerman, Symmetry of forward and reverse path populations, arXiv:1002.2402 (physics.comp-ph), 2010. |
[4] |
E. Darve and E. Ryu, Computing reaction rates in bio-molecular systems using discrete macro-states, Innovations in Biomolecular Modeling and Simulations,1 (2012), 138-206. |
[5] |
A. Dickson and A. R. Dinner., Enhanced Sampling of Nonequilibrium Steady States, Annu. Rev. Phys. Chem., 61 (2010), 441-459. |
[6] |
A. Dickson, A. Warmflash and A. R. Dinner., Separating forward and backward pathways in nonequilibrium umbrella sampling, J. Chem. Phys., 131 (2009), 154104. |
[7] |
A. Dickson, A. Warmflash and A. R. Dinner., Nonequilibrium umbrella sampling in spaces of many order parameters, J. Chem. Phys., 130 (2009), 074104. |
[8] |
W. E and E. Vanden-Eijnden, Towards a Theory of Transition Paths, Journal of Statistical Physics, 123 (2006), 503-523. |
[9] |
G. A. Huber and S. Kim, Weighted ensemble Brownian dynamics simulations for protein association reactions, Biophysical journal, 70 (1996), 97110. |
[10] |
P. Metzner, C. Schütte and E. Vanden-Eijnden, Illustration of transition path theory on a collection of simple examples, The Journal of Chemical Physics, 125 (2006), 084110. |
[11] |
V. S. Pande, K. Beauchamp and G. R. Bowman, Everything you wanted to know about Markov state models but were afraid to ask, Methods, 52 (2010), 99105. |
[12] |
N. Singhal and V. S. Pande, Error analysis and efficient sampling in Markovian state models for molecular dynamics, The Journal of Chemical Physics, 123 (2005), 204909. |
[13] |
W. C. Swope, J. W. Pitera and F. Suits, Describing Protein Folding Kinetics by Molecular Dynamics Simulations. 1. Theory, The Journal of Physical Chemistry B, 108 (2004), 65716581. |
[14] |
E. Vanden-Eijnden, M. Venturoli, G. Ciccotti and R. Elber, On the assumptions underlying milestoning, The Journal of Chemical Physics, 129 (2008), 174102. |
[15] |
E. Vanden-Eijnden and M. Venturoli., Exact rate calculations by trajectory parallelization and tilting, J. Chem. Phys., 131 (2009), 044120. |
[16] |
A. Warmflash, P. Bhimalapuram and A. R. Dinner., Umbrella sampling for nonequilibrium processes, J. Chem. Phys., 127 (2007), 154112. |
[17] |
B. W Zhang, D. Jasnow and D. M. Zuckerman, "Weighted Ensemble Path Sampling for Multiple Reaction Channels," arXiv.org, physics.bio-ph, February 2009. |
[18] |
B. W. Zhang, D. Jasnow and D. M. Zuckerman, The "weighted ensemble" path sampling method is statistically exact for a broad class of stochastic processes and binning procedures, The Journal of Chemical Physics, 132 (2010), 054107. |
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