About WESTPA

Publications

The WESTPA Paper:

  1. MC Zwier, JL Adelman, JW Kaus, AJ Pratt, KF Wong, NB Rego, E Suárez, S Lettieri, DW Wang, M Grabe, DM Zuckerman, and LT Chong. “WESTPA: An interoperable, highly scalable software package for weighted ensemble simulation and analysis”. J. Chem. Theory Comput., 11: 800-809 (2015).

Made with WESTPA:

  1. (1)MC Zwier, JW Kaus, and LT Chong. “Efficient explicit-solvent molecular dynamics simulations of molecular associations: Methane/methane, Na+/Cl-, methane/benzene, and K+/18-crown-6 ether.” J. Chem. Theory Comput., 7: 1189-1197 (2011).

  2. (2)JL Adelman, A Scarbrough, MC Zwier, D Bhatt, LT Chong, DM Zuckerman, and M Grabe. “Simulations of the alternating access mechanism of the sodium symporter Mhp1.” Biophys. J., 101: 2399-2407 (2011).

  3. (3)E Suarez, S Lettieri, MC Zwier, CA Stringer, SR Subramanian, LT Chong and DM Zuckerman. “Simultaneous computation of dynamical and equilibrium information using a weighted ensemble of trajectories.” J. Chem. Theory Comput. 10: 2658-2667 (2014).

  4. (4)JL Adelman and M Grabe. “Simulating rare events using a weighted ensemble-based string method.” J. Chem. Phys., 138: 044105 (2013).

  5. (5)RM Donovan, AJ Sedgewick, JR Faeder and DM Zuckerman. “Efficient stochastic simulation of chemical kinetics networks using a weighted ensemble of trajectories.” J. Chem. Phys., 139: 115105 (2013).

  6. (6)JL Adelman and M Grabe. “Simulating current–voltage relationships for a narrow ion channel using the weighted ensemble method” J. Chem. Theory Comput., 11: 1907-1918 (2015).

Related Weighted Ensemble Publications:

  1. (1)GA Huber and S Kim. "Weighted-ensemble Brownian dynamics simulations for protein association reactions." Biophys. J., 70: 97–110 (1996).

  2. (2)A Rojnuckarin, S Kim, and S Subramaniam. "Brownian dynamics simulations of protein folding: Access to milliseconds time scale and beyond." Proc. Nat. Acad. Sci. USA, 95: 4288–4292 (1998).

  3. (3)A Rojnuckarin, DR Livesay, and S Subramaniam. "Bimolecular reaction simulation using weighted ensemble Brownian dynamics and the University of Houston Brownian dynamics program." Biophys. J., 79: 686-693 (2000).

  4. (4)BW Zhang, D Jasnow, and DM Zuckerman. "Efficient and verified simulation of a path-ensemble for conformational change in a united-residue model of calmodulin." Proc. Nat. Acad. Sci. USA, 104: 18043-18048 (2007).

  5. (5)BW Zhang, D Jasnow, and DM Zuckerman. "The ”weighted ensemble” path sampling method is statistically exact for a broad class of stochastic processes and binning procedures." J. Chem. Phys., 132: 054107 (2010).

  6. (6)D Bhatt, BW Zhang, and DM Zuckerman. "Steady state via weighted ensemble path sampling" J. Chem. Phys., 133: 014110 (2010).

  7. (7)D Bhatt and DM Zuckerman. "Heterogeneous path ensembles for conformational transitions in semiatomistic models of adenylate kinase." J. Chem. Theory Comput., 6: 3527–3539 (2010).

  8. (8)MC Zwier and LT Chong. “Reaching biological timescales with all-atom molecular dynamics simulations.” Curr. Opin. Pharmacol., 10: 745-752 (2010).

  9. (9)D Bhatt and DM Zuckerman. "Beyond microscopic reversibility: Are observable non-equilibrium processes precisely reversible?" J. Chem. Theory Comput., 7: 2520-2527 (2011).

  10. (10)D Bhatt and I Bahar. "An adaptive weighted ensemble procedure for efficient computation of free energies and first passage rates." J. Chem. Phys., 137: 104101 (2012). 

  11. (11)E Darve and E Ryu. "Computing reaction rates in bio-molecular systems using discrete macro-states." Innovations in Biomolecular Modeling and Simulations. Royal Society of Chemistry, 1: 138-206 (2012).

  12. (12)BW Zhang, D Jasnow, and DM Zuckerman. "Weighted ensemble path sampling for multiple reaction channels." arXiv:0902.2772

  13. (13)A Dickson and CL Brooks, III. "WExplore: Hierarchical exploration of high-dimensional spaces using the weighted ensemble algorithm." J. Phys. Chem. B, 138: 3532-3542 (2014). 

  14. (14)B Abdul-Wahid, H Feng, D Rajan, R Costaouec, E Darve, D Thain, and JA Izaguirre. "AWE-WQ: Fast-forwarding molecular dynamics using the accelerated weighted ensemble." J. Chem. Inf. Model., 54: 3033-3043 (2014). 

  15. (15)H Feng, R Costaouec, E Darve and JA Izaguirre. "A comparison of weighted ensemble and Markov state model methodologies." J. Chem. Phys., 142: 214113 (2015). 

  16. (16)A Dickson, AM Mustoe, L Salmon and CL Brooks, III. "Efficient in silico exploration of RNA interhelical conformations using Euler angles and WExplore." Nucl. Acids Res., 42: 12126-12137 (2014).

The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis

Get WESTPAhttps://westpa.github.io/westpa/