X-Pol Potential: An Electronic Structure-Based Force Field for Molecular Dynamics Simulation of a Solvated Protein in Water.
X-Pol Potential: An Electronic Structure-Based Force Field for Molecular Dynamics Simulation of a Solvated Protein in Water.
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DOI：
10.1021/ct800239q
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发表时间：
2009-02-17
影响因子：
5.5
通讯作者：
Gao, Jiali
中科院分区：
文献类型：
--
作者：
Xie, Wangshen;Orozco, Modesto;Truhlar, Donald G.;Gao, Jiali
最近提出的一种称为显式极化 (X-Pol) 电势的基于电子结构的力场用于研究蛋白质中的多体电子极化效应，特别是通过在具有周期性边界条件的水中对牛胰蛋白酶抑制剂 (BPTI) 进行分子动力学 (MD) 模拟。主晶胞是立方体，尺寸约为 54 × 54 × 54 Å3，该晶胞中的原子总数为 14281。近似电子波函数由整个系统的 29026 个基函数组成，经过变分优化，可在每个 MD 步骤中给出最小的 Born-Oppenheimer 能量；这可以有效评估动力学所需的分析力。检查了分子内和分子间极化以及分子内电荷转移效应，发现其显着；例如，58 个主链羰基中有 17 个与中性平均相差超过 0.1 个电子，六个丙氨酸的平均电荷在 -0.05 到 +0.09 之间变化。瞬时超额费用的差异甚至更大；主链羰基的波动净电荷标准差在0.03至0.05之间，超过一半的残基具有标准差超过0.05的过量电荷。我们得出的结论是，新一代 X-Pol 力场允许在比以前更大的系统中包含时间相关的量子力学极化和电荷转移效应。
A recently proposed electronic structure-based force field called the explicit polarization (X-Pol) potential is used to study many-body electronic polarization effects in a protein, in particular by carrying out a molecular dynamics (MD) simulation of bovine pancreatic trypsin inhibitor (BPTI) in water with periodic boundary conditions. The primary unit cell is cubic with dimensions ~54 × 54 × 54 Å3, and the total number of atoms in this cell is 14281. An approximate electronic wave function, consisting of 29026 basis functions for the entire system, is variationally optimized to give the minimum Born–Oppenheimer energy at every MD step; this allows the efficient evaluation of the required analytic forces for the dynamics. Intramolecular and intermolecular polarization and intramolecular charge transfer effects are examined and are found to be significant; for example, 17 out of 58 backbone carbonyls differ from neutrality on average by more than 0.1 electron, and the average charge on the six alanines varies from −0.05 to +0.09. The instantaneous excess charges vary even more widely; the backbone carbonyls have standard deviations in their fluctuating net charges from 0.03 to 0.05, and more than half of the residues have excess charges whose standard deviation exceeds 0.05. We conclude that the new-generation X-Pol force field permits the inclusion of time-dependent quantum mechanical polarization and charge transfer effects in much larger systems than was previously possible.
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影响因子：
3.3
作者：
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通讯作者：
Gao, JL
DOI：
10.1088/0965-0393/5/3/002
发表时间：
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作者：
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