On Easy Implementation of a Variant of the Replica Exchange with Solute Tempering in GROMACS
On Easy Implementation of a Variant of the Replica Exchange with Solute Tempering in GROMACS
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DOI：
10.1002/jcc.21703
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发表时间：
2011-05-01
影响因子：
3
通讯作者：
Takada, Shoji
中科院分区：
文献类型：
--
作者：
Terakawa, Tsuyoshi;Kameda, Tomoshi;Takada, Shoji
为了减少大型系统中传统副本交换方法所需的副本数量，最近提出了溶质回火副本交换（REST）方法。在这里，我们展示了通过重新调整力场参数实现的REST变体可以在不更改代码的情况下使用GROMACS 4执行。我们测试了变体REST的丙氨酸二肽和来自p53的N-末端肽，证实其性能几乎等于原始REST。(C)2010 Wiley Periodicals，Inc. J Comput Chem 32：1228-1234，2011
To reduce the number of replicas required in the conventional replica exchange method for huge systems, recently the replica exchange with solute tempering (REST) method was proposed. Here we showed that a variant of REST realized by rescaling the force-field parameters can be performed with GROMACS 4 without changing the code. We tested the variant REST for alanine dipeptide and an N-terminal peptide from p53 confirming its performance nearly equal to the original REST. (C) 2010 Wiley Periodicals, Inc. J Comput Chem 32: 1228-1234, 2011