Coarse-grained simulation of CAV1-8S in a POPC bilayer

Simulation of CAV1-8S embedded in a symmetric POPC bilayer. The system has 3250 lipids in the protein-proximal leaflet and 3500 lipids in the protein-distal leaflet, counter-ions to neutralize the charges, and was constructed with CHARMM-GUI with initial dimensions of 49 x 49 x 22 nm.

The simulation was run with the MARTINI 2.2 force field at 37C for a total of 8 us. Uploaded are the structure (.gro) file, the centered trajectory (.dcd) from the last 1.5 us (output every 0.3 ns, so a total of 5000 frames), sample simulation parameters (.mdp) and the force field parameters (.itp).

More details and results from the simulation can be found in Doktorova et al. 2025. PNAS. In press (https://doi.org/10.1101/2024.08.28.610209)