Downloads
Here you can find some coordinates and parametric files for our studied systems. The coordinates are either in .pdb or in .gro format. If you use the files for your simulation, please cite the corresponding paper (see Publications section). Surely, we cannot guarantee the files work for you and are free of errors as every model is very specific and probably, the represented models not fully match your requirements and there will be necessity of some change. Anyway, if you find something or there are access problems, please let us know and we will update the files very soon.
| Colloidal systems & Polymers | |
| sds128_w29.gro | United atom starting .gro configuration of sodium dodecyl sulfate(SDS)/water system consisting of 128 SDS and 3750 water molecules (hydration is ~29 water per surfactant). |
| sds512_w29.gro | United atom starting .gro configuration of SDS/water system consisting of 512 SDS and 15000 water molecules (hydration is ~29 water per surfactant). |
| sds512_w29_all_atom.pdb | All atom .pdb initial configuration of SDS/water system consisting of 512 SDS and ~15000 water molecules (~ 29 water per surfactant) developed for NAMD package. |
| sds.itp | Topology file for SDS molecule. |
| Starting configuration with randomly distributed 128 sodium pentadecyl sulfonate (SPDS) molecules in water bulk consisting of 2251 water molecules. | |
| spds128_mic_263mM.gro | The equilibrated 128 SPDS micelle in aqueous solution (263mM SPDS concentration).A united atom .gro file. |
| spds.itp | Topology .itp file for SPDS molecule. |
| United atom coordinate .gro and topology .itp files for Poly vinyl pyrrolidone (PVP) polymer consisting of 408 monomers and 32018 water molecules after 100ns equilibration run. | |
| United atom coordinate .gro and topology .itp file for Poly vinyl alcohol (PVA) polymer consisting of 1024 monomers and 31029 water molecules after 100ns of equilibration run. | |
| Inverse SDS micelle in a mixed toluene/pentanol solvent in the presence of a cationic poly (diallyldimethylammonium chloride) (PDADMAC). Initial configuration all atom .pdb file. | |
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PDADMAC/SDS/Decanol/Water all atom coordinate .pdb after 50ns of run (NAMD package) [see ref.16] |
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micelle_fission.gro |
United atom coordinate .gro file for 192 SPDS/40553 water system after 0.5μs of run. Micelle fission movie is also available. |
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micelle_self_assembly_CG.gro spds_CG.itp micelle_fusion_CG.avi |
Coarse-grained coordinate .gro and topology .itp files for 95SPDS/~5000water system after a couple of microseconds. Micelle fusion movie is available. |
| Biological systems | |
| Dipalmitoyl phosphatidylcholine (DPPC) bilayer all-atom .pdb and CHARMM .psf files (72 lipids with 2393 water molecules, ~33 water per lipid, starting configuration) | |
| DPPC bilayer all-atom .pdb and CHARMM .psf files (128 lipids with 3702 water molecules, ~28 water per lipid, starting configuration) | |
| dppc512_w29.pdb | Starting configuration of 512 DPPC/ 14808 water bilayer. A united atom .pdb file (after a couple of ps run). |
| dppc1024_w30.pdb | Starting configuration of 1024 DPPC/ 31136 water bilayer. A united atom .pdb file. |
| Dimyristoyl phosphatidylcholine (DPPC) bilayer all-atom .pdb and CHARMM .psf files (128 lipids with 3626 water molecules, ~28 water per lipid, starting configuration) | |
| Dipalmitoyl phosphatidylethanolamine (DPPE) bilayer all-atom .pdb and CHARMM .psf files (128 lipids with 4325 water molecules, ~33 water per lipid, starting configuration) | |
| dppc25_dmpc75_w33.pdb | 96 DMPC and 32 DPPC (ratio 3:1) with 4248 water molecules: initial configuration, all atom pdb. |
| dppc50_dmpc50_w33.pdb | 64 DMPC and 64 DPPC (ratio 1:1) with 4253 water molecules: initial configuration, all atom pdb. |
| dppc75_dmpc25_w33.pdb | 32 DMPC and 96 DPPC (ratio 1:3) with 4234 water molecules: initial configuration, all atom pdb. |
| Mixed phospholipid bilayer consisting of 26 POPE (1-palmytoil-2-oleoyl-sn-glycero-3-Phosphatidylethanolamine – 16:0/18:1 PE), 32 SAPE (1-stearoyl-2-arachidonoyl-sn-glycero-3-Phosphatidylethanolamine – 18:0/20:4 PE), 36 POPC (1-palmintoyl-2-oleoyl-sn-glycero-3-Phosphatidylcholine – 16:0/18:1 PC), 34 SOPC (1-stearoyl-2-oleoyl-sn-glycero-3-Phosphatidylcholine – 18:0/18:1 PC) and 2997 water molecules: starting configuration, all atom .pdb and CHARMM .psf files. | |
| PC_PE_mixed_with_prot.pdb | 21 POPE/ 24 SAPE/ 25 POPC/ 24 SOPC/ 2998 water molecules mixed phosholipid bilayer with embedded Glycophorin A protein (transmembrane part): initial configuration, all atom pdb. |
| Human red blood erythrocyte asymmetric model membrane consisting of 252 phospholipids/cholesterol molecules and Glycophorin A protein transmembrane part. (24:0 SM lingoceroyl sphingomyelin (LSM); 16:0 SM hexadecanoyl sphingomyelin (HSM); 1-stearoyl-2-arachidonoyl-sn-glycero-3-phosphatidylserine (SAPS); 1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphatidylserine (SDPS);1-stearoyl-2- 54oleoyl-sn-glycero-3-phosphatidylethanolamine (SOPE); 1-stearoyl-2-arachidonoyl-sn-glycero-phosphatidylethanolamine (SAPE); 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC); 1-stearoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (SOPC); Cholesterol): after 80ns equilibration, all-atom model. | |
We would also like to represent some links where you can find additional data on topologies and coordinates.
Prof. Tieleman’s group (lipid coordinates & topologies)
Computational Molecular Biophysics Group at Georg-August-Universität (lipid/cholesterol complexes)
Professor Mikko Karttunen’s Group (Softsimu, simulation parameters, FF & configuration)
Prof. Siewert-Jan Marrink’s Group (gro, mdp & itp)
Laboratory of Computational Chemistry, Masaryk University (lipids, water, ions, .gro & .top)
Roland Faller Research Group (pdb & gro)