Exploring Protocols to Build Reservoirs to Accelerate Temperature Replica Exchange MD Simulations.
Exploring Protocols to Build Reservoirs to Accelerate Temperature Replica Exchange MD Simulations.
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DOI：
10.1021/acs.jctc.0c00513
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发表时间：
2020-12-08
影响因子：
5.5
通讯作者：
Simmerling C
中科院分区：
文献类型：
--
作者：
Kasavajhala K;Lam K;Simmerling C
温度梯度交换分子动力学（REMD）是一种广泛使用的用于加速生物分子模拟的增强采样方法。在过去的二十年中，已经开发了几种REMD变体，以进一步提高REMD的构象采样率。一种这样的变体，储库REMD（RREMD），被证明可以将构象采样的速率提高约5- 20倍。尽管采样速度显著提高，但RREMD方法尚未被广泛使用，这是由于构建库的困难以及GPU上的代码不可用。在这项工作中，我们将Amber RREMD代码移植到GPU上，使其比CPU代码快20倍。然后，我们探索了构建玻尔兹曼加权储集层和非玻尔兹曼储集层的协议，并测试了每种选择如何影响所得RREMD模拟的准确性。我们表明，使用这里概述的推荐协议，RREMD模拟可以准确地再现通过更昂贵的传统基于温度的REMD模拟获得的玻尔兹曼加权系综，与传统REMD相比，即使对于更大的蛋白质（>50个氨基酸），收敛速度也至少快15倍。
Temperature Replica Exchange Molecular Dynamics (REMD) is a widely used enhanced sampling method for accelerating biomolecular simulations. During the past two decades, several variants of REMD have been developed to further improve the rate of conformational sampling of REMD. One such variant, Reservoir REMD (RREMD), was shown to improve the rate of conformational sampling by around 5–20x. Despite the significant increase in sampling speed, RREMD methods have not been widely used due to the difficulties in building the reservoir and also due to the code not being available on the GPUs. In this work, we ported the Amber RREMD code onto GPUs making it 20x faster than the CPU code. Then, we explored protocols for building Boltzmann-weighted reservoirs as well as non-Boltzmann reservoirs, and tested how each choice affects the accuracy of the resulting RREMD simulations. We show that, using the recommended protocols outlined here, RREMD simulations can accurately reproduce Boltzmann-weighted ensembles obtained by much more expensive conventional temperature-based REMD simulations, with at least 15x faster convergence rates even for larger proteins (>50 amino acids) compared to conventional REMD.
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