THE COMPUTATION OF A POTENTIAL OF MEAN FORCE - CHOICE OF THE BIASING POTENTIAL IN THE UMBRELLA SAMPLING TECHNIQUE
THE COMPUTATION OF A POTENTIAL OF MEAN FORCE - CHOICE OF THE BIASING POTENTIAL IN THE UMBRELLA SAMPLING TECHNIQUE
复制标题
DOI：
10.1063/1.466628
复制
发表时间：
1994-01-15
影响因子：
4.4
通讯作者：
VANGUNSTEREN, WF
中科院分区：
文献类型：
--
作者：
BEUTLER, TC;VANGUNSTEREN, WF
一般来说，柔性分子的构象平衡在溶剂化时发生变化。构象异构体的平衡分布由相关自由度的平均力的潜力决定。然而，由于存在阻碍有效采样的大能量势垒，通过直接的计算机模拟来确定平均力的势通常是不切实际的。为克服与此类障碍相关的问题而经常选择的技术是伞式采样技术。以1,2-二氯乙烷在水中溶剂化的分子动力学模拟为模型，研究了伞形采样技术中偏置势的选择对平均力二面角势计算的影响。比较了单窗口和多窗口技术的效率。对于短仿真周期 (25 ps)，后一种技术比前一种技术表现更好。对于较长的仿真周期，由于周期性边界条件的各向异性引起的系统中发生的其他缓慢过程的采样不足而引起的波动会掩盖性能差异。
Generally, the conformational equilibrium of flexible molecules changes upon solvation. The equilibrium distribution of conformers is determined by the potential of mean force for the relevant degrees of freedom. However, the determination of the potential of mean force by straightforward computer simulation is often impracticable owing to the presence of large energy barriers which prevent efficient sampling. A frequently chosen technique to overcome the problems associated with such barriers is the umbrella sampling technique. Using molecular dynamics simulation of 1,2-dichloroethane solvated in water as a model case, we have investigated the influence of the choice of the biasing potential in the umbrella sampling technique on the computation of the dihedral angle potential of mean force. The efficiencies of one- and multiple-window techniques are compared. For short simulation periods (25 ps) the latter technique performs better than the former. For longer simulation periods the performance difference is obscured by fluctuations caused by insufficient sampling of other slow processes occurring in the system, induced by the anisotropy of the periodic boundary conditions.