Maragliano Luca, Vanden-Eijnden Eric
Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, USA.
J Chem Phys. 2008 May 14;128(18):184110. doi: 10.1063/1.2907241.
A simple, efficient, and accurate method is proposed to map multidimensional free energy landscapes. The method combines the temperature-accelerated molecular dynamics (TAMD) proposed in [L. Maragliano and E. Vanden-Eijnden, Chem. Phys. Lett. 426, 168 (2006)] with a variational reconstruction method using radial-basis functions for the representation of the free energy. TAMD is used to rapidly sweep through the important regions of the free energy landscape and to compute the gradient of the free energy locally at points in these regions. The variational method is then used to reconstruct the free energy globally from the mean force at these points. The algorithmic aspects of the single-sweep method are explained in detail, and the method is tested on simple examples and used to compute the free energy of the solvated alanine dipeptide in two and four dihedral angles.
提出了一种简单、高效且准确的方法来绘制多维自由能景观图。该方法将[L. Maragliano和E. Vanden-Eijnden，《化学物理快报》426, 168 (2006)]中提出的温度加速分子动力学（TAMD）与一种使用径向基函数表示自由能的变分重构方法相结合。TAMD用于快速扫过自由能景观的重要区域，并在这些区域的点上局部计算自由能的梯度。然后使用变分方法从这些点处的平均力全局重构自由能。详细解释了单扫方法的算法方面，并在简单示例上对该方法进行了测试，并用于计算具有两个和四个二面角的溶剂化丙氨酸二肽的自由能。
