String method in collective variables: Minimum free energy paths and isocommittor surfaces
String method in collective variables: Minimum free energy paths and isocommittor surfaces
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DOI：
10.1063/1.2212942
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发表时间：
2006-07-14
影响因子：
4.4
通讯作者：
Ciccotti, Giovanni
中科院分区：
文献类型：
--
作者：
Maragliano, Luca;Fischer, Alexander;Ciccotti, Giovanni
提出了一种计算技术，它结合了弦方法与采样技术，以确定最小自由能路径。该技术只需要计算平均力和另一个条件期望局部沿着的字符串，因此可以应用，即使在自由能计算中保持的集体变量的数量是大的。这与其他自由能采样技术形成对比，其他自由能采样技术旨在映射完整的自由能景观，并且其成本随着自由能中保持的集体变量的数量呈指数级增加。只要集合变量的数量足够大，新技术就可以捕获过渡机制，因为它可以确定反应的提交函数，特别是过渡态区域。新技术的例子说明了丙氨酸二肽，在其中我们计算的异构化过渡使用两个或四个二面角作为集体变量的最小自由能路径。结果表明，使用四个二面角可以捕获的过渡机制，但它不能被捕获仅使用其中的两个。(c)2006年，美国物理学会。
A computational technique is proposed which combines the string method with a sampling technique to determine minimum free energy paths. The technique only requires to compute the mean force and another conditional expectation locally along the string, and therefore can be applied even if the number of collective variables kept in the free energy calculation is large. This is in contrast with other free energy sampling techniques which aim at mapping the full free energy landscape and whose cost increases exponentially with the number of collective variables kept in the free energy. Provided that the number of collective variables is large enough, the new technique captures the mechanism of transition in that it allows to determine the committor function for the reaction and, in particular, the transition state region. The new technique is illustrated on the example of alanine dipeptide, in which we compute the minimum free energy path for the isomerization transition using either two or four dihedral angles as collective variables. It is shown that the mechanism of transition can be captured using the four dihedral angles, but it cannot be captured using only two of them. (c) 2006 American Institute of Physics.