PEACH 4 with ABINIT-MP: a general platform for classical and quantum simulations of biological molecules.
PEACH 4 with ABINIT-MP: a general platform for classical and quantum simulations of biological molecules.
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DOI：
10.1016/j.compbiolchem.2004.01.003
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发表时间：
2004-04
影响因子：
3.1
通讯作者：
Y. Komeiji;Y. Inadomi;T. Nakano
中科院分区：
文献类型：
--
作者：
Y. Komeiji;Y. Inadomi;T. Nakano
开发了生物分子的分子模拟程序包。该包“PEACH version 4 with ABINIT-MP version 20021029”是由ABINIT-MP（片段分子轨道（FMO）法的程序）构建而成的[Chem]。理论物理。Lett. 313(1999) 701]，进入PEACH，一个经典分子动力学模拟（MD）的程序包。演示了该软件包的一些功能。首先，在单点计算中证明了FMO的高并行效率。第二，FMO-MD模拟[化学]。理论物理。Lett. 372(2003) 342]在有和没有明确溶剂的情况下对肽进行了模拟，模拟显示了溶剂对肽电子状态的影响。
A program package for molecular simulations of biological molecules was developed. The package," PEACH version 4 with ABINIT-MP version 20021029," was constructed by incorporating ABINIT-MP, a program for the fragment molecular orbital (FMO) method [Chem. Phys. Lett. 313 (1999) 701], into PEACH, a program package for classical molecular dynamics simulations (MD). A few capabilities of the package were demonstrated. First, high parallel efficiency of FMO was demonstrated in a single point calculation of a protein. Second, FMO-MD simulations [Chem. Phys. Lett. 372 (2003) 342] of a peptide were performed with and without explicit solvent, and the simulations showed the influence of the solvent on the electronic state of the peptide.