Title: Umbrella sampling data of AuNP interacting with a PC bilayer

Type Dataset Heikkilä, Elena, Martinez-Seara, Hector, Gurtovenko, Andrey A., Javanainen, Matti, Häkkinen, Hannu, Vattulainen, Ilpo, Akola, Jaakko (2017): Umbrella sampling data of AuNP interacting with a PC bilayer. Zenodo. Dataset. https://zenodo.org/record/238943

Authors: Heikkilä, Elena (Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland and ‡ COMP Centre of Excellence, Department of Applied Physics, Aalto University, FI-00076 Aalto, Finland) ; Martinez-Seara, Hector (Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland) ; Gurtovenko, Andrey A. (Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoi Prospect 31, V.O., St. Petersburg 199004, Russia and ∥ Department of Molecular Biophysics, Faculty of Physics, St. Petersburg State University, St. Petersburg 198504, Russia) ; Javanainen, Matti (Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland) ; Häkkinen, Hannu (Departments of Physics and Chemistry, Nanoscience Center, University of Jyvaskylä , FI-40014 Jyväskylä , Finland) ; Vattulainen, Ilpo (Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland and &Center for Biomembrane Physics (MEMPHYS), University of Southern Denmark, Odense DK-5230 Denmark) ; Akola, Jaakko (Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland and ‡ COMP Centre of Excellence, Department of Applied Physics, Aalto University, FI-00076 Aalto, Finland and PGI-1, Forschungszentrum Jülich, D-52425 Jülich, Germany) ;

Links

• Item record in Zenodo
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Summary

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

More information

• DOI: 10.5281/zenodo.238943

Dates

• Publication date: 2017
• Issued: January 11, 2017

Rights

• https://creativecommons.org/licenses/by/4.0/legalcode Creative Commons Attribution 4.0 International
• info:eu-repo/semantics/openAccess Open Access

Format

electronic resource

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