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 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.

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.