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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(, top=)
enhanced MD, MD simulations, GPCR, GaMD, membrane proteins, molecular dynamics
enhanced MD, MD simulations, GPCR, GaMD, membrane proteins, molecular dynamics
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