Molecular dynamics simulations of proteins in water without the truncation of long-range Coulomb interactions
Molecular dynamics simulations of proteins in water without the truncation of long-range Coulomb interactions
复制标题
不截断长程库仑相互作用的水中蛋白质的分子动力学模拟
DOI：
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发表时间：
1992
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
开发了一个新的分子动力学模拟程序包COSMOS90，用于模拟由数万个以上原子组成的大分子系统，而不截断远程库仑相互作用。该程序包基于一种新的近似格式（PPPC），可以在不牺牲精度的情况下有效地计算库仑相互作用。在这个近似方案中，距离每个原子较远的电荷群用总电荷和总偶极矩表示。为了评估PPPC的准确性和COSMOS90的能力，使用该程序包对16108个原子（水中溶菌酶）组成的大系统进行了50 ps的分子动力学模拟。每个溶质原子的库仑能计算误差仅为10 A截止近似值的5%（分别为0.9 kcal/mol和18 kcal/mol）。使用COSMOS90进行分子动力学模拟不需要更多的CP…
Abstract A new program package (COSMOS90) for molecular dynamics simulations was developed to simulate large molecular systems consisting of more than tens of thousands of atoms without the truncation of long-range coulomb interactions. This program package was based on a new approximation scheme (PPPC) for calculating efficiently the coulomb interactions without sacrificing accuracy. In this approximation scheme, the group of charges at a long distance from each atom was represented by a total charge and total dipole moment of the group. In order to assess the accuracy of PPPC and the ability of COSMOS90, molecular dynamics simulations were carried out for a large system consisting of 16108 atoms (human lysozyme in water) for 50 ps using this program package. The coulomb energy per solute atom was calculated with only five percent of the error found in the 10 A cut-off approximation (about 0.9 kcal/mol versus 18 kcal/mol, respectively). The molecular dynamics simulations using COSMOS90 require no more CP...