Molecular dynamics simulations of proteins in solution: Artifacts caused by the cutoff approximation
Molecular dynamics simulations of proteins in solution: Artifacts caused by the cutoff approximation
复制标题
溶液中蛋白质的分子动力学模拟：截止近似引起的伪影
DOI：
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发表时间：
1994
期刊：
影响因子：
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通讯作者：
M. Saito
中科院分区：
文献类型：
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作者：
M. Saito
在有/没有截断长程库仑相互作用的情况下，对水中的人体溶菌酶进行了 400 ps 的分子动力学 (MD) 模拟，以研究截断方法引起的人为效应。包括长程库仑相互作用的MD模拟是通过使用最近开发的方法[PPPC方法；摩尔。同时。 8, 321 (1992)]。另一方面，使用 10 A 截止法进行了截断长程库仑相互作用的 MD 模拟。比较这两个结果，发现了以下伪影。截止法导致带电残基与 X 射线结构的偏差比 PPPC 法大 1.7 A。此外，截断方法在水中的平衡结构周围造成了令人无法接受的大波动。然而，PPPC 方法发现的波动与 X 射线 B 因子得出的波动密切相关。
Molecular dynamics (MD) simulations of human lysozyme in water were carried out for 400 ps with/without the truncation of long‐range Coulomb interactions in order to investigate artificial effects caused by the cutoff method. MD simulations with the long‐range Coulomb interactions included were carried out by using a recently developed method [PPPC method; Mol. Simul. 8, 321 (1992)]. On the other hand, MD simulations with the long‐range Coulomb interactions truncated were carried out using the 10 A cutoff method. Comparing both results, the following artifacts were found. The cutoff method caused a 1.7 A larger deviation of charged residues from the x‐ray structure than the PPPC method. Further, the cutoff method caused unacceptably large fluctuation around the equilibrium structure in water. However, the fluctuation found with the PPPC method correlated well with that derived from x‐ray B‐factors.