title: Umbrella sampling data of AuNP interacting with a PC bilayer
author: Heikkilä, Elena
description: Files in Gromacs (v4.6) format used to generate the PMF profile shown in Fig. 3 in [1]. The nanoparticle is pulled to the EC leaflet in the 'genstart' simulations. The initial structures for the umbrella sampling windows are extracted from this trajectory. The files obtained from umbrella sampling windows are named 'pullX.*', where X is the distance between the centers of mass of the AuNP and the EC leaflet phosphori. Trajectories (.xtc) are saved every 100ps. Additionally, the initial and final structures (.gro), the run input files (.tpr), energy files (.edr), log files (.log), checkpoint files (.cpt), simulation parameter files (.mdp), and the files generated by the pull code (pull forces and pull distances, .xvg) are given for each umbrella window. Additionally, an index file (index.ndx) and a topology file (topol.top) common for all systems is provided. TOP.tar contains the molecule definitions (.itp). 'pullf-files.dat' and 'tpr-files.dat' are used by g_wham to extract the profile shown in Fig. 3 (except for the choice of the zero level) by 'g_wham -it tpr-files.dat -if pullf-files.dat -b 40000 -nBootstrap 100' [1] Heikkilä et al., Cationic Au Nanoparticle Binding with Plasma Membrane-like Lipid Bilayers: Potential Mechanism for Spontaneous Permeation to Cells Revealed by Atomistic Simulations, J. Phys. Chem. C, 2014, 118 (20), pp 11131–11141, DOI: 10.1021/jp5024026