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| Main Authors: | , , , , |
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| Format: | Preprint |
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2024
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| Subjects: | |
| Online Access: | https://arxiv.org/abs/2401.05597 |
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| _version_ | 1866914437836832768 |
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| author | Kania, Sagar Webber, Robert J. Simpson, Gideon Aristoff, David Zuckerman, Daniel M. |
| author_facet | Kania, Sagar Webber, Robert J. Simpson, Gideon Aristoff, David Zuckerman, Daniel M. |
| contents | A significant challenge in molecular dynamics (MD) simulations is ensuring that sampled configurations converge to the equilibrium or nonequilibrium stationary distribution of interest. Lack of convergence constrains the estimation of free energies, rates, and mechanisms of complex molecular events. Here, we introduce the "Randomized ITErative trajectory reWeighting" (RiteWeight) algorithm to estimate a stationary distribution from unconverged simulation data. This method iteratively reweights trajectory segments in a self-consistent way by solving for the stationary distribution of a Markov state model (MSM), updating segment weights, and employing a new random clustering in each iteration. The iterative random clustering mitigates the phase-space discretization error inherent in existing trajectory reweighting techniques and yields quasi-continuous configuration-space distributions. We present mathematical analysis of the algorithm's fixed points as well as empirical validation using both synthetic MD Trp-cage trajectories, for which the stationary solution is exactly calculable, and standard atomistic MD Trp-cage trajectories extracted from a long reference simulation. In both test systems, we find that RiteWeight corrects flawed distributions and generates accurate observables for equilibrium and nonequilibrium steady states. The results highlight the value of correcting the underlying trajectory distribution rather than using a standard MSM |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2401_05597 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | RiteWeight: Randomized Iterative Trajectory Reweighting for Steady-State Distributions Without Discretization Error Kania, Sagar Webber, Robert J. Simpson, Gideon Aristoff, David Zuckerman, Daniel M. Computational Physics A significant challenge in molecular dynamics (MD) simulations is ensuring that sampled configurations converge to the equilibrium or nonequilibrium stationary distribution of interest. Lack of convergence constrains the estimation of free energies, rates, and mechanisms of complex molecular events. Here, we introduce the "Randomized ITErative trajectory reWeighting" (RiteWeight) algorithm to estimate a stationary distribution from unconverged simulation data. This method iteratively reweights trajectory segments in a self-consistent way by solving for the stationary distribution of a Markov state model (MSM), updating segment weights, and employing a new random clustering in each iteration. The iterative random clustering mitigates the phase-space discretization error inherent in existing trajectory reweighting techniques and yields quasi-continuous configuration-space distributions. We present mathematical analysis of the algorithm's fixed points as well as empirical validation using both synthetic MD Trp-cage trajectories, for which the stationary solution is exactly calculable, and standard atomistic MD Trp-cage trajectories extracted from a long reference simulation. In both test systems, we find that RiteWeight corrects flawed distributions and generates accurate observables for equilibrium and nonequilibrium steady states. The results highlight the value of correcting the underlying trajectory distribution rather than using a standard MSM |
| title | RiteWeight: Randomized Iterative Trajectory Reweighting for Steady-State Distributions Without Discretization Error |
| topic | Computational Physics |
| url | https://arxiv.org/abs/2401.05597 |