MD simulation of 50-lipid DOPS monolayers in the water-air interface (CHARMM36+OPC4@298.15K)

About these systems: This record contains the simulation files of 50-lipid DOPS monolayers simulated in the water-air interface. The initial strcuture of the systems was assembled using CHARMM-GUI, with sodium counterions to neutralize the system, and equilibrated with GROMACS by following their recommended protocol. The membrane was then compressed and expanded in a simulation using PLUMED, from which states at different values of area per lipid were extracted. Each of these systems was the initial state of a 100 ns long simulation in the NVT ensemble (T=298.15 K), the ones here provided. For all simulations, CHARMM36 parameters for the lipids and the 4-point OPC water model were used. Files provided: Compressed file with all ITP files with the parameters used for the simulations. MDP file used for the production simulations. For each simulation, TOP with the topology, TPR of the simulation, trajectory in TRR format, EDR file, CPT generated and GRO with the final state of the system. All files corresponding to the same simulation are labeled as DOPS_NVT_XX, where XX is the nominal APL at which the simulations were carried out.关于本数据集的模拟体系： 本数据集包含在水-气界面环境中模拟的、由50个DOPS脂质分子构成的单分子层的模拟文件。 本体系的初始结构通过CHARMM-GUI搭建，添加钠离子抗衡离子以中和体系电荷，并遵循其官方推荐流程，使用GROMACS完成平衡模拟。随后借助PLUMED开展模拟，对该单分子层进行压缩与扩张操作，并提取出不同单位脂质面积（area per lipid）下的体系状态。 本次提供的所有体系，均为NVT系综（正则系综，温度T=298.15 K）下时长100 ns的生产模拟的初始状态。所有模拟均采用脂质的CHARMM36力场参数，以及四点OPC水模型（4-point OPC water model）。 数据集包含的文件如下： 存储所有模拟所用参数的ITP文件的压缩归档文件。 生产模拟所用的MDP参数文件。 针对每一次模拟，均包含拓扑结构文件TOP、模拟二进制输入文件TPR、TRR格式的轨迹文件、能量数据文件EDR、检查点文件CPT，以及记录体系最终状态的GRO文件。所有属于同一次模拟的文件均以"DOPS_NVT_XX"命名，其中XX为该模拟所采用的标称单位脂质面积数值。