This repository contains the files required to repeat Molecular Dynamics simulations of the closed glycine receptor alpha2 (GlyR alpha2) homopentamer in an 80% POPC and 20% cholesterol lipid bilayer. These simulations were performed using the GROMOS 54a7 united atom ForceField with GROMACS v2023.
Publication pending.
The S285 folder contains files for the Wild-type GlyR alpha2 homopentamer simulations in the closed state.
The P285 folder contains files for the S285P mutant of GlyR alpha2 homopentamer simulations in the closed state.
Included files:
.
|__S285
| |__run1
| | |__GlyRa2_closed_S285_POPC_CLR_r1_start.gro
| | |__GlyRa2_closed_S285_POPC_CLR_r1.top
| | |__GlyRa2_closed_S285_POPC_CLR_r1.ndx
| | |__GlyRa2_closed_S285_POPC_CLR_r1.tpr
| |
| |__run2
| | |__GlyRa2_closed_S285_POPC_CLR_r2_start.gro
| | |__GlyRa2_closed_S285_POPC_CLR_r2.top
| | |__GlyRa2_closed_S285_POPC_CLR_r2.ndx
| | |__GlyRa2_closed_S285_POPC_CLR_r2.tpr
| |
| |__run3
| |__GlyRa2_closed_S285_POPC_CLR_r3_start.gro
| |__GlyRa2_closed_S285_POPC_CLR_r3.top
| |__GlyRa2_closed_S285_POPC_CLR_r3.ndx
| |__GlyRa2_closed_S285_POPC_CLR_r3.tpr
|
|__P285
| |__run1
| | |__GlyRa2_closed_P285_POPC_CLR_r1_start.gro
| | |__GlyRa2_closed_P285_POPC_CLR_r1.top
| | |__GlyRa2_closed_P285_POPC_CLR_r1.ndx
| | |__GlyRa2_closed_P285_POPC_CLR_r1.tpr
| |
| |__run2
| | |__GlyRa2_closed_P285_POPC_CLR_r2_start.gro
| | |__GlyRa2_closed_P285_POPC_CLR_r2.top
| | |__GlyRa2_closed_P285_POPC_CLR_r2.ndx
| | |__GlyRa2_closed_P285_POPC_CLR_r2.tpr
| |
| |__run3
| |__GlyRa2_closed_P285_POPC_CLR_r3_start.gro
| |__GlyRa2_closed_P285_POPC_CLR_r3.top
| |__GlyRa2_closed_P285_POPC_CLR_r3.ndx
| |__GlyRa2_closed_P285_POPC_CLR_r3.tpr
|
|
|__gromos54a7.ff # Contains the force field files required to repeat the simulations.
|
|__prod.mdp # Molecular Dynamics parameters file to repeat the Molecular Dynamics simulations with Gromacs v2023.