MD data for Transient interactions between cationic ionizable lipids and anionic lipids foster lamellar to hexagonal phase transition

The data stored in this repository is part of the journal article: Coarse-grained molecular dynamics simulations of mixtures of DOPS:DODMA:DOPE (25:25:50) (prefix=dops_dodma_dope), DODMA:DOPE (50:50) (prefix=dodma_dope), DOPS:DOPE (50:50) (prefix=dops_dope), PI3P12:DODMA:DOPE (12.5:37.5:50) (prefix=pi3p12_dodma_dope), PI3P25:DODMA:DOPE (25:25:50) (prefix=pi3p25_dodma_dope), and PI3P:DOPE (50:50) (prefix=pi3p_dope) as well as DOPS:DODMA:CHOL (25:25:50) (prefix=dops_dodma_chol), DODMA:CHOL (50:50) (prefix=dodma_chol), DOPS:CHOL (50:50) (prefix=dops_chol) using the Martini 2.2 force field with polarizable water. Provided are the coarse-grained parametrizations, the starting frames ([prefix]_md_0.gro) and the resulting trajectories ([prefix]_md.xtc) of each run, the repesctive gromacs input files, and the respective topologies. The directories indicated as "openmm" contain the starting frames ([prefix]_md_0.gro) and the resulting trajectories ([prefix]_md.xtc) of each run and the openmm input file run.py. The runs containing PI3P are separated from those containing DOPS. equilibration_input: Contains the gromacs input files for the equilibration procedure at several temperatures 270K 285K 300K 315K production_input: Contains the gromacs input files for the production at several temperatures for all three simulations sets. 270K 285K 300K 315K DOPS containing runs: simulation_set_1: Contains the data provided for simulation set 1. runs_1wpl: Simulations at 1 water bead per lipid (w/l) 270K, 270K_contaniso 285K, 285K_contaniso 300K, 300K_contaniso, 300K_openmm 315K, 315K_contaniso, 315K_openmm runs_2wpl: Simulations at 2 w/l 270K, 270K_contaniso 285K, 285K_contaniso 300K, 300K_contaniso, 300K_openmm 315K, 315K_contaniso, 315K_openmm runs_3wpl: Simulations at 3 w/l 270K 285K, 285K_openmm 300K, 300K_openmm 315K, 315K_openmm runs_4wpl: Simulations at 4 w/l 270K 285K 300K 315K simulation_set_2: Contains all data provided for simulation set 2. runs_2wpl_300K: Simulations at 2 w/l and 300 K dodma_dope: Contains 10 replicate runs dops_dodma_dope: Contains 10 replicate runs dops_dope: Contains 10 replicate runs runs_2wpl_315K: Simulations at 2 w/l and 315 K dodma_dope: Contains 10 replicate runs dops_dodma_dope: Contains 10 replicate runs dops_dope: Contains 10 replicate runs simulation_set_3: Contains all data provided for simulation set 3. runs_2wpl_315K: Simulations at 2 w/l and 315 K dodma_dope: Contains 1 run dops_dodma_dope: Contains 2 replicate runs PI3P containing runs: simulation_set_1_pi3p: Contains the data provided for simulation set 1. runs_1wpl: Simulations at 1 water bead per lipid (w/l) 270K, 270K_contaniso 285K, 285K_contaniso 300K, 300K_contaniso 315K, 315K_contaniso runs_2wpl: Simulations at 2 w/l 270K, 270K_contaniso 285K, 285K_contaniso 300K, 300K_contaniso 315K, 315K_contaniso runs_3wpl: Simulations at 3 w/l 270K 285K, 285K_openmm 300K, 300K_contaniso 315K, 315K_contaniso runs_4wpl: Simulations at 4 w/l 270K 285K 300K 315K simulation_set_2_pi3p: Contains all data provided for simulation set 2. runs_2wpl_300K: Simulations at 2 w/l and 300 K pi3p_dope: Contains 10 replicate runs pi3p12_dodma_dope: Contains 10 replicate runs pi3p25_dodma_dope: Contains 10 replicate runs runs_2wpl_315K: Simulations at 2 w/l and 315 K pi3p_dope: Contains 10 replicate runs pi3p12_dodma_dope: Contains 10 replicate runs pi3p25_dodma_dope: Contains 10 replicate runs simulation_set_3_pi3p: Contains all data provided for simulation set 3. runs_2wpl_315K: Simulations at 2 w/l and 315 K pi3p12_dodma_dope: Contains 2 replicate runs Cholesterol contaning runs: simulation_set_1_chol: Contains the data provided for simulation set 1. runs_1wpl: Simulations at 1 water bead per lipid (w/l) 270K 285K 300K 315K runs_2wpl: Simulations at 2 w/l 270K 285K 300K 315K runs_3wpl: Simulations at 3 w/l 270K 285K 300K 315K runs_4wpl: Simulations at 4 w/l 270K 285K 300K 315K