256 DPPC Molecules bilayer in pure Water, simulated at 288K (gel) or 358K (fluid)

Publication: MLLPA: A Machine Learning-assisted Python module to study phase-specific events in lipid membranes

Published on: 08 April 2021

Journal: J Comp Chem, 2021, DOI: 10.1002/jcc.26508

Description: Simulation files used to train our Python module to identify the thermodynamic phase of individual lipid molecules in a bilayer, as well as the simulation files analysed by the machine learning models. More information on the module can be found on its website.

The training files are named dppc_gel.gro and dppc_fluid.gro. They respectively correspond to the final frame of the systems simulated at 288K and 358K. All other files are the files analysed by the module.

System composition:

DPPC molecules: 256 with 130 atoms each

Water molecules:  42,492 with 3 atoms each 

Simulation box dimensions (approx.): 9 x 9 x 20 nm

Simulation details:

Software: Gromacs (v. 2020)

Forcefield: Charmm36 (v. June 2015) - Water: TIP3P

Thermostat: Nose-hoover (0.4ps, 2 groups)

Barostat: Parrinello-Rahman semi-isotropic (2.0ps, 1.0 bar on each axis, 4.5e-5 bar-1)

Duration: 25 ns (after stabilisation)