Data for: "Solvent-controlled self-assembly of Fmoc protected aliphatic amino acids"

The following data is contained within this entry (as described by folder): Fmoc-Amino_Acids > contains the trajectories and run files associated with each Fmoc amino acid both in the distinguished by THF content * run (0 – 80), within this are two sub-directories (charged and neutral) which refer to the charge state of the C-terminus in that simulation. System topologies and index files used can be found in the directory box_* (0 – 80) directory. More detail is provided in the README.txt file. itp_files > Structure files associated with each FmocSAA, as well as the parameter files used for the Martini simulation bead types etc. scripts > contains all analysis and setup scripts used to generate the simulation structures, exuctue their simulation on the Archie West HPC and analyse the results obtained from the trajectories. Further detail is available in the README.txt file. structures > these are the relevant *gro and *pdb files used to build the starting structures. UB_sampling_files > Files used for Umbrella Sampling to determine what bead was best for modelling THF. These were adapted from the Martini tutorial on the same subject which can be found here (http://cgmartini.nl/index.php/tutorials-general-introduction-gmx5/partitioning-techniques)

本条目包含如下按文件夹分类的数据：Fmoc-氨基酸（Fmoc-Amino_Acids）文件夹：包含与每种Fmoc氨基酸相关的轨迹文件与运行配置文件，所有数据按四氢呋喃（THF）含量及运行编号（0–80）分组；该文件夹下设两个子目录（charged与neutral），分别对应模拟中C端的带电与中性电荷状态。所用的系统拓扑文件与索引文件可在box_*（0–80）目录中找到。更多详细信息请参见README.txt文件。itp文件（itp_files）文件夹：包含与每种FmocSAA相关的结构文件，以及用于Martini模拟的珠型参数文件等。脚本（scripts）文件夹：包含所有用于生成模拟结构、在Archie West高性能计算集群（HPC）上执行模拟以及分析轨迹所得结果的分析与设置脚本。更多详细信息请参见README.txt文件。结构文件（structures）文件夹：包含用于构建初始结构的相关*.gro与*.pdb文件。伞形采样文件（UB_sampling_files）文件夹：包含用于伞形采样的文件，用于确定最适合建模四氢呋喃（THF）的珠型；这些文件改编自同主题的Martini教程，教程链接为http://cgmartini.nl/index.php/tutorials-general-introduction-gmx5/partitioning-techniques