期刊
COMPUTER PHYSICS COMMUNICATIONS
卷 180, 期 2, 页码 276-301出版社
ELSEVIER
DOI: 10.1016/j.cpc.2008.08.008
关键词
Molecular dynamics; Electrostatics; Polarization; Induced point dipoles; Thole; Car-Parrinello type of dynamics; Biomolecules
资金
- Genopole-France
The MDVRY classical molecular dynamics package is presented for the study of biomolecules in the gas and liquid phase. Electrostatic polarization has been implemented in the formalism of point induced dipoles following the model of Thole. Two schemes have been implemented for the calculation of induced dipoles, i.e. resolution of the self-consistent equations and a 'Car-Parrinello' dynamical approach. In this latter, the induced dipoles are calculated at each time step of the dynamics through the dynamics of additional degrees of freedom associated with the dipoles. This method saves computer time and allows to study polarized solvated proteins at a very low CPU cost. The program is written in C-language and runs on LINUX machines. A detailed manual of the code is given. The main features of the package are illustrated taking on examples of proteins in the gas phase or immersed in liquid water.
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据