Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
J Comput Chem. 2010 Apr 30;31(6):1333-43. doi: 10.1002/jcc.21415.
We present an algorithm to reconstruct atomistic structures from their corresponding coarse-grained (CG) representations and its implementation into the freely available molecular dynamics (MD) program package GROMACS. The central part of the algorithm is a simulated annealing MD simulation in which the CG and atomistic structures are coupled via restraints. A number of examples demonstrate the application of the reconstruction procedure to obtain low-energy atomistic structural ensembles from their CG counterparts. We reconstructed individual molecules in vacuo (NCQ tripeptide, dipalmitoylphosphatidylcholine, and cholesterol), bulk water, and a WALP transmembrane peptide embedded in a solvated lipid bilayer. The first examples serve to optimize the parameters for the reconstruction procedure, whereas the latter examples illustrate the applicability to condensed-phase biomolecular systems.
我们提出了一种从粗粒化（CG）表示重建原子结构的算法，并将其实现到免费的分子动力学（MD）程序包 GROMACS 中。该算法的核心部分是一个模拟退火 MD 模拟，其中 CG 和原子结构通过约束耦合。许多例子证明了该重建程序可以将低能原子结构集合从其 CG 对应物中获得。我们重建了真空（NCQ 三肽、二棕榈酰磷脂酰胆碱和胆固醇）、本体水和嵌入溶剂化脂质双层中的 WALP 跨膜肽中的单个分子。第一个例子用于优化重建程序的参数，而后面的例子则说明了其在凝聚相生物分子系统中的适用性。
