MD dataset for EGFR TMJM dimer in ordered membrane with GM3

EGFR Molecular Dynamics Trajectories ## Dataset Description This dataset contains molecular dynamics simulation trajectories investigating the inhibitory mechanism of GM3 ganglioside on EGFR (Epidermal Growth Factor Receptor) activation. THis is the second replicate. ## File Contents ### Trajectory Files - `EGFR_dimer_in_ordered_membrane.xtc` - Trajectory of EGFR TM-JM dimer peptides in GM3-containing membrane (10 μs) ### Structure Files - `step5_assembly.psf` - Protein structure file for GM3-containing system ## Simulation Details ### System Composition - **Membrane dimensions**: 40 × 40 nm - **Proteins**: 4 EGFR TM-JM peptides (residues 610-659; two dimers) - **ordered membrane system**: CHOL:DLiPC:SM = 33:33:33 mol% (upper leaflet); CHOL:DLiPC:DOPS = 33:33:33 mol% (lower leaflet) ### Simulation Parameters - **Force field**: MARTINI 2.2 coarse-grained - **Software**: GROMACS 2023.3 - **Temperature**: 298 K - **Pressure**: 1 bar (semi-isotropic coupling) - **Salt concentration**: 150 mM NaCl - **Duration**: 10 μs per system ## Usage These trajectories can be analyzed using standard molecular dynamics analysis tools: ```bash # Example: Load with MDAnalysis (Python) import MDAnalysis as mda # Load GM3-containing system u_gm3 = mda.Universe('with_GM3.psf', 'with_GM3.xtc') # Load GM3-free system u_free = mda.Universe('without_GM3.psf', 'without_GM3.xtc') # Codes for analyses on the manuscript by Sato and Tamagaki-Asahina Codes for analyses are available on github, https://github.com/takeshi-sato-dev/