BAD-NEUS: Rapidly converging trajectory stratification
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arXiv
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| Main Authors: | , , , |
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| Format: | Preprint |
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2024
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| _version_ | 1866913467636645888 |
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| author | Strahan, John Lorpaiboon, Chatipat Weare, Jonathan Dinner, Aaron R. |
| author_facet | Strahan, John Lorpaiboon, Chatipat Weare, Jonathan Dinner, Aaron R. |
| contents | An issue for molecular dynamics simulations is that events of interest often involve timescales that are much longer than the simulation time step, which is set by the fastest timescales of the model. Because of this timescale separation, direct simulation of many events is prohibitively computationally costly. This issue can be overcome by aggregating information from many relatively short simulations that sample segments of trajectories involving events of interest. This is the strategy of Markov state models (MSMs) and related approaches, but such methods suffer from approximation error because the variables defining the states generally do not capture the dynamics fully. By contrast, once converged, the weighted ensemble (WE) method aggregates information from trajectory segments so as to yield unbiased estimates of both thermodynamic and kinetic statistics. Unfortunately, errors decay no faster than unbiased simulation in WE as originally formulated and commonly deployed. Here we introduce a theoretical framework for describing WE that shows that introduction of an approximate stationary distribution on top of the stratification, as in nonequilibrium umbrella sampling (NEUS), accelerates convergence. Building on ideas from MSMs and related methods, we generalize the NEUS approach in such a way that the approximation error can be reduced systematically. We show that the improved algorithm can decrease simulation times required to achieve a desired precision by orders of magnitude. |
| format | Preprint |
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arxiv_https___arxiv_org_abs_2404_19653 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | BAD-NEUS: Rapidly converging trajectory stratification Strahan, John Lorpaiboon, Chatipat Weare, Jonathan Dinner, Aaron R. Statistical Mechanics Computational Physics An issue for molecular dynamics simulations is that events of interest often involve timescales that are much longer than the simulation time step, which is set by the fastest timescales of the model. Because of this timescale separation, direct simulation of many events is prohibitively computationally costly. This issue can be overcome by aggregating information from many relatively short simulations that sample segments of trajectories involving events of interest. This is the strategy of Markov state models (MSMs) and related approaches, but such methods suffer from approximation error because the variables defining the states generally do not capture the dynamics fully. By contrast, once converged, the weighted ensemble (WE) method aggregates information from trajectory segments so as to yield unbiased estimates of both thermodynamic and kinetic statistics. Unfortunately, errors decay no faster than unbiased simulation in WE as originally formulated and commonly deployed. Here we introduce a theoretical framework for describing WE that shows that introduction of an approximate stationary distribution on top of the stratification, as in nonequilibrium umbrella sampling (NEUS), accelerates convergence. Building on ideas from MSMs and related methods, we generalize the NEUS approach in such a way that the approximation error can be reduced systematically. We show that the improved algorithm can decrease simulation times required to achieve a desired precision by orders of magnitude. |
| title | BAD-NEUS: Rapidly converging trajectory stratification |
| topic | Statistical Mechanics Computational Physics |
| url | https://arxiv.org/abs/2404.19653 |