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

<p>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.&nbsp;</p><p>Files include:</p><p>CCL1_CCR8_noSer23_oriented_repaired1_system.pdb : system topology</p><p>CCL1_CCR8_config.xml : config for running GaMD-OpenMM</p><p>CCL1_CCR8_N_1ns_imaged_structure.pdb : initial topology/structure</p><p>CCL1_CCR8_N_1ns_imaged_trajectory.dcd : trajectory file</p><p>&nbsp;</p><p>Simulations can be loaded in python using MDTraj:</p><p>import mdtraj</p><p>trj = mdtraj.load(&lt;dcd file&gt;, top=&lt;pdb file&gt;)</p>