title: Coarse-grained simulations of lipid membranes with various concentrations of embedded proteins
author: Javanainen, Matti
description: Membranes with a polydisperse set of proteins with lipid/protein ratios of 50 (lp50), 75 (lp75), 100 (lp100), 200 (lp200), and 400 (lp400) are simulated for 100 µs. The protein–protein interactions are scaled down to prevent excessive aggregation.  For all simulated lipid/protein ratio, a trajectory (.xtc) file is stored every 10 ns. Note that water beads and ions have been removed for a smaller file size. All beads, including solvent ones, are present in initial and final structures (.gro). Energy terms are stored every 1 ns (.edr). Simulation run input files (.tpr) and checkpoint files (.cpt) enable the rerunning or continuation of the simulations. Topology (.top) and index (.ndx) files for each system are also provided. The topology files for scaled protein–protein interactions work as follows: The bead types of the proteins in their topology files (.itp) are changed to those with a 'p', for example P4–>P4p. The interactions between normal beads are listed in martini_v2.2_standard.itp, while the interactions among 'p' beads as well as the cross terms between 'p' beads and normal beads are given in martini_v2.2_scaled_80.itp. The force constant of the elastic network was increased to enable an integration time step of 20 fs. The lipid head groups are gently restrained in the direction normal to the membrane to prevent excessive fluctuations and they hence simulate the presence of an actin cytoskeleton. The simulation parameters, common for all systems, are listed in the file md.mdp.  All files are compatible with Gromacs 5.0. The results extracted from these simulations are presented in the paper M. Javanainen, H. Martinez-Seara, R. Metzler, and I. Vattulainen; Diffusion of Integral Membrane Proteins in Protein-Rich Membranes. J. Phys. Chem. Lett., 2017, 8 (17), pp 4308–4313, DOI: 10.1021/acs.jpclett.7b01758 The Martini topologies are obtained form http://cgmartini.nl