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>)