Thermostat artifacts in replica exchange molecular dynamics simulations.
Thermostat artifacts in replica exchange molecular dynamics simulations.
复制标题
DOI：
10.1021/ct800557h
复制
发表时间：
2009
影响因子：
5.5
通讯作者：
Hummer, Gerhard
中科院分区：
文献类型：
--
作者：
Rosta, Edina;Buchete, Nicolae-Viorel;Hummer, Gerhard
我们探讨了恒温器在复制交换分子动力学（REMD）模拟的影响。对于不产生正则系综的恒温器，REMD模拟被发现扭曲的配置空间分布。对于散装水，我们发现小的偏差的平均势能，积累的尾巴的势能分布，和人工之间的相关性的能量在不同的温度。如果溶质存在，如在蛋白质折叠模拟中，其构象平衡可以改变。在弱耦合（Berendsen）恒温器的螺旋形成肽的REMD模拟中，我们发现折叠状态在低温下过度填充约10%，在高温下填充不足。结果，折叠焓偏离正确值几乎3千卡/摩尔。这种人口转变的原因是，非正则系综与狭窄的势能波动人为地偏向于副本之间的交换低能量折叠结构在高温和高能量展开结构在低温。我们的结论是，REMD模拟应该只与产生一个典型的合奏恒温器一起进行。
We explore the effects of thermostats in replica exchange molecular dynamics (REMD) simulations. For thermostats that do not produce a canonical ensemble, REMD simulations are found to distort the configuration-space distributions. For bulk water, we find small deviations of the average potential energies, the buildup of tails in the potential energy distributions, and artificial correlations between the energies at different temperatures. If a solute is present, as in protein folding simulations, its conformational equilibrium can be altered. In REMD simulations of a helix-forming peptide with a weak-coupling (Berendsen) thermostat, we find that the folded state is overpopulated by about 10% at low temperatures, and underpopulated at high temperatures. As a consequence, the enthalpy of folding deviates by almost 3 kcal/mol from the correct value. The reason for this population shift is that non-canonical ensembles with narrowed potential energy fluctuations artificially bias toward replica exchanges between low-energy folded structures at the high temperature and high-energy unfolded structures at the low temperature. We conclude that REMD simulations should only be performed in conjunction with thermostats that produce a canonical ensemble.
登录
查看更多内容
影响因子：
4.4
作者：
Sindhikara, Daniel;Meng, Yilin;Roitberg, Adrian E.
通讯作者：
Roitberg, Adrian E.
影响因子：
2.9
作者：
HOOVER, WG
通讯作者：
HOOVER, WG
影响因子：
4.4
作者：
JORGENSEN, WL;CHANDRASEKHAR, J;KLEIN, ML
通讯作者：
KLEIN, ML
影响因子：
4.4
作者：
ESSMANN, U;PERERA, L;PEDERSEN, LG
通讯作者：
PEDERSEN, LG
DOI：
10.1073/pnas.2232868100
发表时间：
2003-11-25
影响因子：
11.1
作者：
Nymeyer, H;García, AE
通讯作者：
García, AE