Grossfield Alan, Feller Scott E, Pitman Michael C
IBM T. J. Watson Research Center, Yorktown Heights, New York 10598, USA.
Proteins. 2007 Apr 1;67(1):31-40. doi: 10.1002/prot.21308.
The central question in evaluating almost any result from a molecular dynamics simulation is whether the calculation has converged. Unfortunately, assessing the ergodicity of a single trajectory is very difficult to do. In this work, we assess the sampling of molecular dynamics simulations of the membrane protein rhodopsin by comparing the results from 26 independent trajectories, each run for 100 ns. By examining principal components and cluster populations, we show that rhodopsin's fluctuations are not well described by 100 ns of dynamics, and that the sampling is not fully converged even for individual loops. The results serve as a reminder of the caution required when interpreting molecular dynamics simulations of macromolecules.
评估分子动力学模拟的几乎任何结果时的核心问题是计算是否已经收敛。不幸的是，评估单个轨迹的遍历性非常困难。在这项工作中，我们通过比较26条独立轨迹（每条轨迹运行100纳秒）的结果来评估膜蛋白视紫红质的分子动力学模拟的采样情况。通过检查主成分和聚类种群，我们表明视紫红质的波动不能通过100纳秒的动力学很好地描述，并且即使对于单个环，采样也没有完全收敛。这些结果提醒我们在解释大分子的分子动力学模拟时需要谨慎。
