Optimization of partial multicanonical molecular dynamics simulations applied to an alanine dipeptide in explicit water solvent.
Optimization of partial multicanonical molecular dynamics simulations applied to an alanine dipeptide in explicit water solvent.
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应用于显性水溶剂中的丙氨酸二肽的部分多规范分子动力学模拟的优化。
DOI：
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发表时间：
2011
期刊：
影响因子：
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通讯作者：
H. Okumura
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文献类型：
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作者：
H. Okumura
部分多谐算法适用于分子动力学和蒙特卡罗模拟样品的大范围势能的重要组成部分。虽然它是一种强有力的生物分子结构预测技术，但部分势能的选择并没有得到优化。为了找到最佳选择，对丙氨酸二肽在明确的水溶剂中进行了部分多电子分子动力学模拟，并对部分势能进行了15个试验选择。最佳选择是溶质原子间的静电势能、伦纳德-琼斯势能和扭转角势能之和。在这种情况下，局部多谐模拟采样了P（II）、C(5)、α(R)、α(P)、α(L)和C态的所有局部最小自由能态，并且访问这些态的频率最高。此外，骨干二面角φ和ψ旋转非常好。在这三个项中最重要的项是静电势能，并且Lennard-Jones项也有助于克服空间限制。另一方面，多范式模拟对所有六种状态进行采样，但访问这些状态的次数较少。传统的规范模拟只采样了六种状态中的四种：P(II)， C(5), α(R)和α(P)状态。
The partial multicanonical algorithm for molecular dynamics and Monte Carlo simulations samples a wide range of an important part of the potential energy. Although it is a strong technique for structure prediction of biomolecules, the choice of the partial potential energy has not been optimized. In order to find the best choice, partial multicanonical molecular dynamics simulations of an alanine dipeptide in explicit water solvent were performed with 15 trial choices for the partial potential energy. The best choice was found to be the sum of the electrostatic, Lennard-Jones, and torsion-angle potential energies between solute atoms. In this case, the partial multicanonical simulation sampled all of the local-minimum free-energy states of the P(II), C(5), α(R), α(P), α(L), and C states and visited these states most frequently. Furthermore, backbone dihedral angles ϕ and ψ rotated very well. It is also found that the most important term among these three terms is the electrostatic potential energy and that the Lennard-Jones term also helps the simulation to overcome the steric restrictions. On the other hand, multicanonical simulation sampled all of the six states, but visited these states fewer times. Conventional canonical simulation sampled only four of the six states: The P(II), C(5), α(R), and α(P) states.
DOI：
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发表时间：
1997-11
期刊：
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影响因子：
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作者：
Anders Irbäck;Carsten Peterson;F. Potthast;Erik Sandelin
通讯作者：
Anders Irbäck;Carsten Peterson;F. Potthast;Erik Sandelin