Article ; Online: DeepWEST: Deep Learning of Kinetic Models with the Weighted Ensemble Simulation Toolkit for Enhanced Sampling.
Journal of chemical theory and computation
2023 Volume 19, Issue 4, Page(s) 1342–1359
Abstract: ... sampling of the potential energy surface has a significant impact on the performance of WE, i.e ...
| Abstract | Recent advances in computational power and algorithms have enabled molecular dynamics (MD) simulations to reach greater time scales. However, for observing conformational transitions associated with biomolecular processes, MD simulations still have limitations. Several enhanced sampling techniques seek to address this challenge, including the weighted ensemble (WE) method, which samples transitions between metastable states using many weighted trajectories to estimate kinetic rate constants. However, initial sampling of the potential energy surface has a significant impact on the performance of WE, i.e., convergence and efficiency. We therefore introduce deep-learned kinetic modeling approaches that extract statistically relevant information from short MD trajectories to provide a well-sampled initial state distribution for WE simulations. This hybrid approach overcomes any statistical bias to the system, as it runs short unbiased MD trajectories and identifies meaningful metastable states of the system. It is shown to provide a more refined free energy landscape closer to the steady state that could efficiently sample kinetic properties such as rate constants. |
|---|---|
| Language | English |
| Publishing date | 2023-01-31 |
| Publishing country | United States |
| Document type | Journal Article |
| ISSN | 1549-9626 |
| ISSN (online) | 1549-9626 |
| DOI | 10.1021/acs.jctc.2c00282 |
| Database | MEDical Literature Analysis and Retrieval System OnLINE |
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