The RED scheme: Rate-constant estimation from pre-steady state weighted ensemble simulations
The RED scheme: Rate-constant estimation from pre-steady state weighted ensemble simulations
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DOI：
10.1063/5.0041278
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发表时间：
2021-03-21
影响因子：
4.4
通讯作者：
Chong, Lillian T.
中科院分区：
文献类型：
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作者：
DeGrave, Alex J.;Bogetti, Anthony T.;Chong, Lillian T.
我们提出了从事件持续时间（RED）计划，一个新的计划，更有效地计算速率常数使用加权系综路径采样策略的速率。该方案使速率常数估计从较短的轨迹，将事件持续时间的概率分布，或跨越障碍的时间，从模拟。我们已经应用了RED计划加权合奏模拟的各种罕见事件的过程，范围在复杂性：蛋白质构象转换的残留水平模拟，原子模拟Na+/Cl-协会在明确的溶剂，和原子模拟蛋白质-蛋白质协会在明确的溶剂。速率常数估计高达50%以上的效率比原来的加权系综方案。重要的是，我们的计划帐户的系统误差，结果从统计偏差对观察事件的持续时间短，并相应地重新加权的事件持续时间分布。RED方案与任何涉及长度与最可能事件持续时间相似的无偏轨迹的模拟策略相关，包括加权集合、里程碑和标准模拟以及Markov状态模型的构建。
We present the Rate from Event Durations (RED) scheme, a new scheme that more efficiently calculates rate constants using the weighted ensemble path sampling strategy. This scheme enables rate-constant estimation from shorter trajectories by incorporating the probability distribution of event durations, or barrier-crossing times, from a simulation. We have applied the RED scheme to weighted ensemble simulations of a variety of rare-event processes that range in complexity: residue-level simulations of protein conformational switching, atomistic simulations of Na+/Cl- association in explicit solvent, and atomistic simulations of protein-protein association in explicit solvent. Rate constants were estimated with up to 50% greater efficiency than the original weighted ensemble scheme. Importantly, our scheme accounts for the systematic error that results from statistical bias toward the observation of events with short durations and reweights the event duration distribution accordingly. The RED scheme is relevant to any simulation strategy that involves unbiased trajectories of similar length to the most probable event duration, including weighted ensemble, milestoning, and standard simulations as well as the construction of Markov state models.