Graph-based analyses of dynamic water-mediated hydrogen-bond networks in phosphatidylserine:cholesterol membranes

Published: 13 August 2023| Version 1 | DOI: 10.17632/h8y6zjckcw.1
Contributor:
Honey Jain

Description

Molecular dynamics simulations of POPS lipid bilayers with and without cholesterol.

Files

Steps to reproduce

Simulation details: Software and version: NAMD 2.13 Forcefield and version: CHARMM, c36 Jul 2020 Time step : 1.0 fs Coordinates saved every : 1ns Accumulated simulation time : Last 100ns of 500ns long trajectory Temperature: 310.15K Pressure: 1 bar System setup: Solvent type: TIP3P 0.15M neutralizing KCl salt System 1: pure POPS Number of molecules: Water: 8578 POPS (in each bilayer):109 Total number of atoms: 53680 System 2: POPS_Chol Number of molecules: Water: 8367 POPS (in each bilayer): 98 Cholesterol (in each bilayer): 11 Total number of atoms: 51859

Institutions

Universitatea din Bucuresti, Freie Universitat Berlin

Categories

Molecular Dynamics

Funding

European Union’s Horizon 2020 research and innovation programme

860592

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