Zavadlav Julija, Melo Manuel N, Cunha Ana V, de Vries Alex H, Marrink Siewert J, Praprotnik Matej
Laboratory for Molecular Modeling, National Institute of Chemistry , Hajdrihova 19, SI-1001 Ljubljana, Slovenia.
Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 7, 9747 AG Groningen, Netherlands.
J Chem Theory Comput. 2014 Jun 10;10(6):2591-8. doi: 10.1021/ct5001523. Epub 2014 May 6.
We present adaptive resolution molecular dynamics simulations of aqueous and apolar solvents using coarse-grained molecular models that are compatible with the MARTINI force field. As representatives of both classes of solvents we have chosen liquid water and butane, respectively, at ambient temperature. The solvent molecules change their resolution back and forth between the atomistic and coarse-grained representations according to their positions in the system. The difficulties that arise from coupling to a coarse-grained model with a multimolecule mapping, for example, 4-to-1 mapping in the case of the Simple Point Charge (SPC) and MARTINI water models, could be successfully circumvented by using bundled water models. We demonstrate that the presented multiscale approach faithfully reproduces the structural and dynamical properties computed by reference fully atomistic molecular dynamics simulations. Our approach is general and can be used with any atomistic force field to be linked with the MARTINI force field.
我们使用与MARTINI力场兼容的粗粒度分子模型，展示了水性和非极性溶剂的自适应分辨率分子动力学模拟。作为这两类溶剂的代表，我们分别选择了常温下的液态水和丁烷。溶剂分子根据其在系统中的位置，在原子级和粗粒度表示之间来回改变其分辨率。例如，在简单点电荷（SPC）和MARTINI水模型中，与具有多分子映射（如4比1映射）的粗粒度模型耦合时出现的困难，可以通过使用捆绑水模型成功规避。我们证明，所提出的多尺度方法忠实地再现了通过参考全原子分子动力学模拟计算得到的结构和动力学性质。我们的方法具有通用性，可与任何要与MARTINI力场链接的原子力场一起使用。
