Computational protocol: Dicationic Alkylammonium Bromide Gemini Surfactants. Membrane Perturbation and Skin Irritation

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Protocol publication

[…] All MD simulations were carried out in the NpT ensemble and under periodic boundary conditions, using the GROMACS package, version 3.3.3–, and the GROMOS 96 53a6 force field , . A standard time step of 2 fs was used for both the equilibration and production runs. Non-bonded interactions were computed on the basis of a neighbor list, updated every 10 steps. Long-range electrostatics were computed using the particle mesh Ewald (PME) method, as recommended for charged membrane simulations . For Lennard-Jones energies, a cut-off of 1.4 nm was applied. Temperature and pressure were coupled to the Berendsen external baths maintained at 325 K (ca. 10 K above the gel to liquid crystalline phase transition of DPPC) and 1 bar (semi-isotropic pressure coupling, separately applied to the plane and direction), with coupling constants of 0.1 and 0.5 ps, respectively.To obtain a starting configuration, each system was firstly subjected to an energy minimization step. The system were then left to evolve up to 100 ns, using the LINCS algorithm to keep bonds containing H atoms under positional restraint conditions. The first 40 ns were considered sufficient to attain equilibrated systems (converged value of the area per lipid), while the last 60 ns of production runs were subsequently subjected to standard analysis, such as atom-atom (group-group) distance distributions and radial distribution functions (rdf). MD trajectories were visualized, and configuration images extracted using the VMD 1.8.6 software . […]

Pipeline specifications

Software tools GROMACS, P-LINCS, VMD
Application Protein structure analysis
Organisms Homo sapiens
Diseases Genetic Diseases, Inborn, Drug-Related Side Effects and Adverse Reactions