Implementation of a Serial Replica Exchange Method in a Physics-Based United-Residue (UNRES) Force Field.
Implementation of a Serial Replica Exchange Method in a Physics-Based United-Residue (UNRES) Force Field.
复制标题
在基于物理的联合保留（UNRER RER RER RER RER RER RER RER RER RER RER RES）中实施串行复制交换方法。
DOI：
10.1021/ct800063d
复制
发表时间：
2008-08-01
影响因子：
5.5
通讯作者：
Scheraga, Harold A.
中科院分区：
文献类型：
--
作者：
Shen, Hujun;Czaplewski, Cezary;Liwo, Adam;Scheraga, Harold A.
利用复制交换法（REM）可以克服模拟蛋白质折叠时的动力学捕获问题。然而，在分子动力学模拟中实现REM时，需要并行计算机上处理器之间的同步，处理器之间的通信限制了其在复杂系统中有效采样构象空间的能力。为了最大限度地减少模拟过程中处理器之间的通信，Hagan等人最近提出了串行副本交换方法（SREM）。化学。[j] .生物工程学报，2007,31(2):444 - 444。在这里，我们报告了这种新的SREM算法与我们的基于物理的联合残余（UNRES）力场的实现。该方法已在蛋白1E0L上进行了温度无关的UNRES力场测试，并在终端阻断的十丙氨酸（Ala10）和1GAB上进行了温度相关的UNRES力场测试。使用与温度无关的力场，SREM再现了REM的结果，但在时钟时间方面效率更高，并且在分布式内存机器上可伸缩性更好。然而，将SREM精确应用于温度相关的UNRES算法需要确定UNRES能量分量的四维分布，而不是每个温度的一维能量分布，这是非常昂贵的。因此，我们假设力场的温度依赖性对邻近温度可以忽略。该版本的SREM适用于Ala10，这是一个简单的系统，但无法再现热力学结果，以及更复杂的1GAB蛋白上的常规REM。因此，SREM可以应用于温度无关的UNRES力场，但不适用于温度相关的UNRES力场。
The kinetic-trapping problem in simulating protein folding can be overcome by using a Replica Exchange Method (REM). However, in implementing REM in molecular dynamics simulations, synchronization between processors on parallel computers is required, and communication between processors limits its ability to sample conformational space in a complex system efficiently. To minimize communication between processors during the simulation, a Serial Replica Exchange Method (SREM) has been proposed recently by Hagan et al. (J. Phys. Chem. B 2007, 111, 1416–1423). Here, we report the implementation of this new SREM algorithm with our physics-based united-residue (UNRES) force field. The method has been tested on the protein 1E0L with a temperature-independent UNRES force field and on terminally blocked deca-alanine (Ala10) and 1GAB with the recently introduced temperature-dependent UNRES force field. With the temperature-independent force field, SREM reproduces the results of REM but is more efficient in terms of wall-clock time and scales better on distributed-memory machines. However, exact application of SREM to the temperature-dependent UNRES algorithm requires the determination of a four-dimensional distribution of UNRES energy components instead of a one-dimensional energy distribution for each temperature, which is prohibitively expensive. Hence, we assumed that the temperature dependence of the force field can be ignored for neighboring temperatures. This version of SREM worked for Ala10 which is a simple system but failed to reproduce the thermodynamic results as well as regular REM on the more complex 1GAB protein. Hence, SREM can be applied to the temperature-independent but not to the temperature-dependent UNRES force field.
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影响因子：
2.8
作者：
Hansmann, UHE
通讯作者：
Hansmann, UHE
影响因子：
3.3
作者：
Khalili, M;Liwo, A;Scheraga, HA
通讯作者：
Scheraga, HA
DOI：
10.1080/01621459.1995.10476590
发表时间：
1995-09-01
影响因子：
3.7
作者：
GEYER, CJ;THOMPSON, EA
通讯作者：
THOMPSON, EA
影响因子：
3.3
作者：
Hagen, Morten;Kim, Byungchan;Berne, B. J.
通讯作者：
Berne, B. J.
DOI：
10.1073/pnas.0408885102
发表时间：
2005-02-15
影响因子：
11.1
作者：
Liwo, A;Khalili, M;Scheraga, HA
通讯作者：
Scheraga, HA