|All files which are available for download here are exclusively for non-commercial, scientific use. If you want to use them commercially please contact us.
You are required to cite the corresponding publication(s) in any work you publish based on them. Some of the models base on existing models from other groups, they have to be cited as well.
These files work(ed) for us but we cannot guarantee they work for you.
- Systematically coarse–grained Polyisoprene and Polystyrene: tar.gz file containing all relevant data as input for md_spherical
Reference: Qi Sun, and Roland Faller: Systematic coarse-graining of a polymer blend: Polyisoprene and Polystyrene J Chem Theor Comp 2(3) 607-615 (2006)
This model was also used in:
Qi Sun, and Roland Faller: Phase Separation in Polyisoprene/Polystyrene Blends by a Systematically Coarse-Grained Model J Chem Phys 126(14) 144908 (2007)
- Phosphatidic Acid:
POPA bilayer configuration containing 128 lipids, counterions and salt in SPC water,
Gromacs.gro file POPA forcefield, Gromacs.itp file. The force-field bases partially on the so-called Berger force-field, the headgroup charges are calculated using quantum chemistry. The configuration originally was derived from a POPC simulation by the Tieleman group and after changing the model simulated for roughly 80 ns. For details please check the reference.
Original reference: Allison N. Dickey, and Roland Faller: Examining the Contributions of Lipid Shape and Head Group Charge on Bilayer Behavior Biophys J 95(6) 2636-2646 (2008)
The model was also used in:
Allison N. Dickey, and Roland Faller: Behavioral Differences between Phosphatidic Acid and Phosphatidylcholine in the presence of the Nicotinic Acetylcholine Receptor Biophys J 95(12) 5637-5647 (2008)
- Texas Red DHPE:
Bilayer configuration containing 128 lipids (1 TR–DHPE and 127 DPPC), counterion in SPC water, Protein data bank .pdb file, TR-DHPE forcefield, Gromacs .itp fileThe forcefield also bases partially on the so–called Berger force-field, the Texas Red headgroup charges are calculated using quantum chemistry. For details please check the
Original Reference: Michael J. Skaug, Marjorie L. Longo, and Roland Faller: Computational Studies of Texas Red DHPE – Model Building and Applications J Phys Chem B 113(25) 8758-8766 (2009)
The model was also used in:
Michael J. Skaug, Marjorie L. Longo, Roland Faller: The Impact of Texas Red on Lipid Bilayer Properties J Phys Chem B 115(26) 8500-8505 (2011)
- Systematically coarse-grained Polythiophene (P3HT) and Fullerene:Input files in LAMMPS format. Reference: David M. Huang, Roland Faller, Khan Do, Adam J. Moule: Coarse-grained computer simulations of polymer/fullerene bulk heterojunctions for organic photovoltaic applications J Chem Theor Comp 6(2) 527-537 (2010)
The model was also used in:
David M. Huang, Adam J. Moule, Roland Faller: Characterization of Polymer-Fullerene Mixtures for Organic Photovoltaics by Systematically Coarse Grained Molecular Simulation Fluid Phase Equilibria 302 (1-2) 21-25 (2011)
- Ceramide mixtures: Bilayer configuration containing 616 lipids (208 : 208 : 200 ternary mixture of ceramide NS (24:0), cholesterol, and free fatty acid., i.e. lignoceric acid), in SPC water, Protein data bank .pdb file
Fatty acid forcefield, Gromacs .itp file
Ceramide forcefield, Gromacs .itp file
Oleic Acid forcefield, Gromacs .itp file
Reference: Matthew I. Hoopes, Massimo Noro, Marjorie L. Longo, and Roland Faller: Bilayer Structure and Lipid Dynamics in a Model Stratum Corneum with Oleic Acid J Phys Chem B 115(12) 3164-3171 (2011)
- Ergosterol Model:
Ergosterol forcefield, Gromacs .itp fileReference: Juan M. Vanegas, Marjorie L. Longo, and Roland Faller: Crystalline, Ordered and Disordered Lipid Membranes: Convergence of Stress Profiles due to Ergosterol J Am Chem Soc 133(11) 3720-3723 (2011)
- Pegylated DOPC (DOPC–PEG): MARTINI DOPC-PEG forcefield (mix of pegylated and unpegylated lipids and water), Gromacs .top fileOriginal Reference: Shouh–Chuang Yang, and Roland Faller: Pressure and Surface Tension Control Self-Assembled Structures in Mixtures of Pegylated and Non–Pegylated Lipids Langmuir 28(4) 2275-2280 (2012)
The model was also used to study tethered bilayers in:
Chueh Liu, Roland Faller: Conformational, Dynamical and Tensional Study of Tethered Bilayer Lipid Membranes in Coarse-Grained Molecular Simulations Langmuir 28(45) 15907–15915 (2012)
- MTSL modified DPPC (DPPC-MTSL)
DPPC lipid with MTSL spinlabel forcefield Gromacs .itp file
127 DPPC + 2 labeled DPPC_MTSL Configuration Gromacs.gro file
The force-field bases on the 43A1-S3 force-field combined with Quantum Chemistry for the Spinlabel. For details see the reference.
Reference: Sabrina Kemmerer, John C. Voss, Roland Faller: Molecular Dynamics Simulation of Dipalmitoylphosphatidylcholine modified with a MTSL nitroxide spin label in a lipid membrane Biochimica et Biophysica Acta (Biomembranes) 1828(11) 2770–2777 (2013) (DOI 10.1016/j.bbamem.2013.07.030)
- Butanol Coarse-graining Tutorial:
Necessary data in a tar.gz file
These are the materials needed to perform the Butanol coarse-graining tutorial described in the book chapter below.
Reference: Roland Faller: Systematic Coarse Graining of Polymers and Biomolecules in Multiscale Modelling Methods for Applications in Materials Science (ISBN 978-3-89336-899-0) pages 135-150: Editors: Ivan Kondov and Godehard Sutmann, Schriften des FZ Jülich, IAS Series Volume 19, 2013
- Plant Sterols and Glucosylceramide
DLiPC Gromacs .itp file
Glucosylceramide Gromacs .itp file
Sitosterol Gromacs .itp file
Example configuration containing DLiPC, Glucosylceramide and Sitosterol Gromacs .gro file
Reference: Shiva Emami, Sodeif Azadmard-Damirchi, Seyed Hadi Peighambardoust, Javad Hesari, Hadi Valizadeh, Roland Faller: Molecular Dynamics Simulations of Ternary Lipid Bilayers Containing Plant Sterol and Glucosylceramide Chemistry and Physics of Lipids 203, 24-32 (2017) (DOI 10.1016/j.chemphyslip.2017.01.003)
- Reactive modeling of alkoxysilanes
ReaxFF force field parameters for simulating polycondensation of alkoxysilanes. Force field parameters were optimized using a parallel optimization scheme using a combination of experimental and quantum chemistry data In this parameter set C, O, and Si represent the elements carbon, oxygen, and silicon. Hydrogen is represented with two atom types: “H” and “Hc”. “H” parameters represent hydroxyl hydrogens present in silanol, alcohol, or water. “Hc” parameters are used to represent nonpolar hydrocarbon hydrogens.
Joshua D. Deetz, Roland Faller: Parallel Optimization of a Reactive Force Field for Polycondensation of Alkoxysilanes J Phys Chem B 118 (37) 10966–10978 (2014) (DOI 10.1021/jp504138r)
Other groups which publish force-fields include:
Tieleman group at University of Calgary
Karttunen group at University of Western Ontario