Large Popc Monolayer Simulations With Charmm36+Opc @ 298 K (Part 2/2)

POPC monolayers simulated at a varying area per lipid in the NVT ensemble. The Charmm36 lipid model [1] is employed together with the 4-point OPC water model [2]. Each system contains two monolayers with 256 lipids each. These monolayers are separated by a water slab, and surrounded by vacuum. The number in the filename corresponds to the area per lipid in Ångströms. The starting structures were generated by setting up a system with an area per lipid of 50 Å^2, followed by a simulation during which the monolayer area was expanded using PLUMED. All trajectories, 100 ns long, are simulated with Gromacs 5.0.x [3] using the default Charmm36 monolayer simulations parameters given in the mdp file. This mdp file, together with the topology (.top) and index files (common for all simulations) can be downloaded from Part 1 of this upload (see below). The topologies (.itp) for the lipids can be obtained from Charmm-GUI and for the OPC water model from https://bioinformatics.cs.vt.edu/~izadi/ . Part 1 of this upload is available at: https://doi.org/10.5281/zenodo.322830 The data are discussed in the related publication: Matti Javanainen, Antti Lamberg, Lukasz Cwiklik, Ilpo Vattulainen, and O. H. Samuli Ollila. <em>Atomistic Model for Nearly Quantitative Simulations of Langmuir Monolayers</em>, Langmuir <strong>2018</strong> 34 (7), 2565-2572, DOI: 10.1021/acs.langmuir.7b02855 [1] DOI: 10.1021/jp101759q<br> [2] DOI: 10.1021/jz501780a<br> [3] DOI: 10.1016/j.softx.2015.06.001本数据集为在正则系综（NVT）下以可变单位脂质面积模拟得到的1-棕榈酰-2-油酰-sn-甘油-3-磷酸胆碱（POPC）单分子层体系。本模拟采用Charmm36脂质力场模型[1]与四点OPC水模型[2]。每个模拟体系包含两层单分子层，每层含256个脂质分子；两层单分子层之间由水层隔开，整体体系外围设置真空环境。 文件名中的数字对应单位脂质面积，单位为埃（Å）。初始结构通过构建单位脂质面积为50 Ų的体系生成，随后借助PLUMED工具开展模拟，逐步扩张单分子层面积。 所有时长为100 ns的模拟轨迹均通过Gromacs 5.0.x [3]完成，模拟参数采用mdp文件中预设的Charmm36单分子层模拟默认参数。该mdp文件、拓扑结构文件（.top）以及通用索引文件（适用于所有模拟）可从本上传资源的第一部分获取（详见下文）。脂质分子的拓扑结构文件（.itp）可从Charmm-GUI获取，OPC水模型的拓扑结构文件可从https://bioinformatics.cs.vt.edu/~izadi/ 下载。 本上传资源的第一部分可通过以下链接获取：https://doi.org/10.5281/zenodo.322830 本数据集相关研究成果已发表于以下论文： Matti Javanainen、Antti Lamberg、Lukasz Cwiklik、Ilpo Vattulainen与O. H. Samuli Ollila。*用于朗缪尔单分子层近乎定量模拟的全原子力场模型*，*Langmuir*（《朗缪尔》），2018年，第34卷第7期，2565-2572页，DOI: 10.1021/acs.langmuir.7b02855 [1] DOI: 10.1021/jp101759q [2] DOI: 10.1021/jz501780a [3] DOI: 10.1016/j.softx.2015.06.001