Quantifying configuration-sampling error in Langevin simulations of complex molecular systems Journal Article
| Authors: | Fass, J.; Sivak, D. A.; Crooks, G. E.; Beauchamp, K. A.; Leimkuhler, B.; Chodera, J. D. |
| Article Title: | Quantifying configuration-sampling error in Langevin simulations of complex molecular systems |
| Abstract: | While Langevin integrators are popular in the study of equilibrium properties of complex systems, it is challenging to estimate the timestep-induced discretization error: the degree to which the sampled phase-space or configuration-space probability density departs from the desired target density due to the use of a finite integration timestep. Sivak et al., introduced a convenient approach to approximating a natural measure of error between the sampled density and the target equilibrium density, the Kullback-Leibler (KL) divergence, in phase space, but did not specifically address the issue of configuration-space properties, which are much more commonly of interest in molecular simulations. Here, we introduce a variant of this near-equilibrium estimator capable of measuring the error in the configuration-space marginal density, validating it against a complex but exact nested Monte Carlo estimator to show that it reproduces the KL divergence with high fidelity. To illustrate its utility, we employ this new near-equilibrium estimator to assess a claim that a recently proposed Langevin integrator introduces extremely small configuration-space density errors up to the stability limit at no extra computational expense. Finally, we show how this approach to quantifying sampling bias can be applied to a wide variety of stochastic integrators by following a straightforward procedure to compute the appropriate shadow work, and describe how it can be extended to quantify the error in arbitrary marginal or conditional distributions of interest. © 2018 by the authors. |
| Keywords: | sampling error; langevin dynamics; langevin integrators; kl divergence; molecular dynamics integrators; integrator error; baoab; velocity verlet with velocity randomization (vvvr); bussi-parrinello; shadow work; nonequilibrium free energy |
| Journal Title: | Entropy |
| Volume: | 20 |
| Issue: | 5 |
| ISSN: | 1099-4300 |
| Publisher: | MDPI |
| Date Published: | 2018-05-01 |
| Start Page: | 318 |
| Language: | English |
| DOI: | 10.3390/e20050318 |
| PROVIDER: | scopus |
| PMCID: | PMC6208357 |
| PUBMED: | 30393452 |
| DOI/URL: | |
| Notes: | Entropy -- Cited By :2 -- Export Date: 2 January 2019 -- Article -- Source: Scopus C7 |
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