Gaussian-accelerated Molecular Dynamics simulations of CCR8-CCL1-Gprotein complex in a POPC lipid bilayer

Gaussian-accelerated Molecular Dynamics simulations of the CCR8-CCL1-Gprotein complex in a POPC lipid bilayer. Simulation system was prepared with OpenMM v7.7 and simulations were performed using the GaMD-OpenMM package (https://github.com/MiaoLab20/gamd-openmm) with a modification to include the MDTraj h5 file formate reporter as the output file format. These simulations were then converted to pdb topologies and dcd trajectories using MDTraj. Files include: CCL1_CCR8_noSer23_oriented_repaired1_system.pdb : system topology CCL1_CCR8_config.xml : config for running GaMD-OpenMM CCL1_CCR8_N_1ns_imaged_structure.pdb : initial topology/structure CCL1_CCR8_N_1ns_imaged_trajectory.dcd : trajectory file Simulations can be loaded in python using MDTraj: import mdtraj trj = mdtraj.load(<dcd file>, top=<pdb file>)本数据集针对POPC脂质双分子层中的CCR8-CCL1-G蛋白复合物开展了高斯加速分子动力学（Gaussian-accelerated Molecular Dynamics, GaMD）模拟。 模拟体系通过OpenMM v7.7构建，模拟运行采用GaMD-OpenMM工具包（https://github.com/MiaoLab20/gamd-openmm）完成，该工具包经修改后支持将MDTraj的h5文件格式作为输出报告格式。 随后通过MDTraj将上述模拟结果转换为pdb拓扑文件与dcd轨迹文件。 数据集包含以下文件： - CCL1_CCR8_noSer23_oriented_repaired1_system.pdb：模拟体系拓扑文件 - CCL1_CCR8_config.xml：GaMD-OpenMM运行配置文件 - CCL1_CCR8_N_1ns_imaged_structure.pdb：初始拓扑与结构文件 - CCL1_CCR8_N_1ns_imaged_trajectory.dcd：轨迹文件 可通过Python调用MDTraj加载模拟轨迹： import mdtraj trj = mdtraj.load(<dcd file>, top=<pdb file>)