Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy and European Laboratory for Non-linear Spectroscopy (LENS), Via Nello Carrara 1, I-50019 Sesto Fiorentino, Italy.
J Chem Phys. 2014 Feb 14;140(6):064104. doi: 10.1063/1.4863999.
An important limitation of unidirectional nonequilibrium simulations is the amount of realizations of the process necessary to reach suitable convergence of free energy estimates via Jarzynski's relationship [C. Jarzynski, Phys. Rev. Lett. 78, 2690 (1997)]. To this regard, an improvement of the method has been achieved by means of path-breaking schemes [R. Chelli et al., J. Chem. Phys. 138, 214109 (2013)] based on stopping highly dissipative trajectories before their normal end, under the founded assumption that such trajectories contribute marginally to the work exponential averages. Here, we combine the path-breaking scheme, called probability threshold scheme, to bidirectional nonequilibrium methods for free energy calculations [G. E. Crooks, Phys. Rev. E 61, 2361 (2000); R. Chelli and P. Procacci, Phys. Chem. Chem. Phys. 11, 1152 (2009)]. The method is illustrated and tested on a benchmark system, i.e., the helix-coil transition of deca-alanine. By using path-breaking in our test system, the computer time needed to carry out a series of nonequilibrium trajectories can be reduced up to a factor 4, with marginal loss of accuracy in free energy estimates.
单向非平衡模拟的一个重要限制是，为了通过 Jarzynski 关系[C. Jarzynski, Phys. Rev. Lett. 78, 2690 (1997)]达到自由能估计的适当收敛，需要进行大量的过程实现。为了解决这个问题，已经通过开创性的方案[R. Chelli 等人，J. Chem. Phys. 138, 214109 (2013)]提高了该方法的效率，这些方案基于在正常结束之前停止高度耗散的轨迹，前提是这些轨迹对工作指数平均值的贡献微不足道。在这里，我们将称为概率阈值方案的开创性方案与用于自由能计算的双向非平衡方法相结合[G. E. Crooks, Phys. Rev. E 61, 2361 (2000); R. Chelli 和 P. Procacci, Phys. Chem. Chem. Phys. 11, 1152 (2009)]。该方法在基准系统上进行了说明和测试，即癸氨酸的螺旋-卷曲转变。通过在我们的测试系统中使用开创性方案，可以将进行一系列非平衡轨迹所需的计算机时间减少多达 4 倍，而自由能估计的准确性略有下降。
