Improving the replica-exchange molecular-dynamics method for efficient sampling in the temperature space.
Improving the replica-exchange molecular-dynamics method for efficient sampling in the temperature space.
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DOI：
10.1103/physreve.91.052708
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发表时间：
2015-05
期刊：
影响因子：
--
通讯作者：
Changjun Chen;Yi Xiao;Yanzhao Huang
中科院分区：
文献类型：
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作者：
Changjun Chen;Yi Xiao;Yanzhao Huang
复制交换分子动力学（REMD）是分子模拟中常用的一种采样方法。通过在不同温度下频繁地交换复制品，分子可以跳出最小值并在构象空间中有效地采样。尽管REMD在许多应用中已被证明是实用的，但它确实有一个严重的局限性。所有温度下的所有复制品必须在复制品交换步骤之间的一段时间内进行模拟。这对于具有高自由能势垒的反应可能是有问题的。在这种情况下，模拟中需要太多的副本。为了减少计算量，提高其性能，本文提出了一种改进的REMD方法。在模拟过程中，每个温度下的每个副本可以保持在活动或非活动状态，并且仅在交换步骤中在状态之间切换。在激活状态下，复制品通过正常的分子动力学在正则系综中自由移动，而在非激活状态下，复制品暂时冻结，直到下一个交换步骤。处于活动状态的副本（活动副本）的数量取决于计算机中的CPU数量。使用额外的非活动副本，可以在更广泛的温度空间中执行REMD模拟。实际应用表明，修正的REMD方法是可靠的。与标准REMD方法相比，在相同数量的活性副本的情况下，该REMD方法可以在自由能最小值周围产生更合理的自由能表面。
Replica-exchange molecular dynamics (REMD) is a popular sampling method in the molecular simulation. By frequently exchanging the replicas at different temperatures, the molecule can jump out of the minima and sample efficiently in the conformational space. Although REMD has been shown to be practical in a lot of applications, it does have a critical limitation. All the replicas at all the temperatures must be simulated for a period between the replica-exchange steps. This may be problematic for the reaction with high free energy barriers. In that case, too many replicas are required in the simulation. To reduce the calculation quantity and improve its performance, in this paper we propose a modified REMD method. During the simulation, each replica at each temperature can stay in either the active or inactive state and only switch between the states at the exchange step. In the active state, the replica moves freely in the canonical ensemble by the normal molecular dynamics, and in the inactive state, the replica is frozen temporarily until the next exchange step. The number of the replicas in the active states (active replicas) depends on the number of CPUs in the computer. Using the additional inactive replicas, one can perform an REMD simulation in a wider temperature space. The practical applications show that the modified REMD method is reliable. With the same number of active replicas, this REMD method can produce a more reasonable free energy surface around the free energy minima than the standard REMD method.