生物分子水溶液的Monte Carlo模拟 III.力偏倚抽样法和Metropolis抽样法的比较

本文采用先前所用的一个中性丙氨酸分子加56个水分子的体系,对力偏倚(FB)抽样法和Metropolis抽样法进行了比较.发现用FB法,由体系的晶体点阵构型出发到达平衡态所需的循环数为Metropolis法的五分之二.为了得到较好的结构信息所需的构型数也仅为后者的五分之二.虽然每个循环所需机时为Metropolis法的1.6倍,仍是一加速收敛的好方法.本文进一步支持了以分子的平移扩散作为判别抽样效率的判据,指出接受几率在0.33——0.36之间的步长可能是合适的.此外还统计了和丙氨酸作用大于2keal/mol的分子的坚标,使它们与丙氨酸—水分子径向分布图的峰值相对应.

MONTE CARLO SIMULATION ON AQUEOS SOLUTION OF BIOLOGICAL MOLECULES III. A COMPARISON BETWEEN PORCE BIAS SCHEME

A force bias MC (FBMC) simulation was performed on a system of 56 water molecules and one neutral alanine molecule, which is identical with the one we used previously in Metropolis MC (MMC)simulation. Comparing the results with those of Metropolis sampling we found that the cycle numbers needed for equilibration and extraction of structural information are about 2/5 of that by Metropolis scheme. Aelthough the CPU time of each cycle in FBMC is 1.6 times that in MMC, FB schem is still an effective method for convergence acceleration. This study shows that the translational diffusion is a good criterion for judging sampling efficiency, and suggests that the step size making the acceptance rate between 0.33 and 0.36 may be suitable.