title: Short molecular dynamics of a peptide inside a pure DMPC membrane
author: davide cruz
description: 1 ns of molecular dynamics simulation of a 19-residue peptide inside a pure DMPC membrane, performed at the NPT ensemble - 1 atm at 310K using Berendsen (semi-isotropic) and V-rescale for pressure and temperature coupling, respectively, with 1.6 ps and 0.1ps as coupling constants. Van der Waals interactions were treated using the Verlet algorithm with a 1 nm cutoff. Electrostatics where treated with particle-mesh Ewald, with a 1 nm cutoff for the real space calculations. Both the peptide and DMPC were parameterized using the GROMOS 54A7, while SPC was used for water. LINCS restraints were used on all the bonds. Peptide sequence is AAAQAAQAQWAQRQATWQA. This sequence was not taken from any real world examples, as this is a test system created for MDAnalysis datasets. The peptide was set to have be α-helical secondary structure, and was inserted manually in the membrane before minimization and equilibration. More on MDAnalysis: https://www.mdanalysis.org/