Coarse-grained MD simulation provenance of membrane embedded GPCR using GROMACS and aiida-gromacs

Example setup of a martini2 coarse-grained molecular dynamics simulation of the active state PTH2R (Parathyroid hormone receptor type 2) protein embedded in a lipid bilayer membrane along with water and counter-ions. Command-line tools provided in aiida-gromacs are used to track each step performed on the terminal.

The data:

The files in this zenodo record are:

1144.dot.pdf: The image of the graph representation for the simulation workflow.

gpcr_all_steps.aiida: The aiida archive file where all simulation setup steps performed in this work are packaged.

run_commands.sh: The script used to produce the provenance data for this system.

inputs_only.zip: Simulation setup input files for the 'run_commands.sh' script.

The output files produced from the aiida-gromacs provenance tool used to collect the simulation steps for the are in the following files:

1_protein.zip: Output files for the retrieval and cleaning up of the protein structure.

2_martinize.zip: Output files for the protein coarse graining steps.

3_insane.zip: Output files for building the lipid bilayer membrane around the coarse-grained protein.

4_gromacs.zip: Output files for the ionisation steps in gromacs.

5_gromacs.zip: Output files for minimisation, equilibration and production simulation of the simulated system.

The stripped trajectory for the active and inactive states of PTH2R are in the following files:

R1a.pdb and R1a.xtc: pdb and trajectory of coordinates for the active state protein.

R1i.pdb and R1i.xtc: pdb and trajectory of coordinates for the inactive state protein.