cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.633598
title: Molecular dynamics simulation trajectory of a fully hydrated DMPC lipid bilayer

description: <strong>System: </strong>DMPC (dimyristoylphosphatidylcholine) bilayer in water. <strong>Number of lipids: </strong>128.<br> <strong>Number of waters:</strong> 5097. <strong>Lipid model:</strong> 'Berger' united-atom [<em>Biophys. J.</em> <strong>72</strong> 2002 (1997)].<br> <strong>Water model:</strong> SPC [In <em>Intermolecular Forces,</em> ed. Pullman. 331 (1981)]. <strong>Simulation engine:</strong> Gromacs 3.x [www.gromacs.org] <strong>Trajectory length:</strong> 110 ns.<br> <strong>Previously equilibrated for:</strong> 20 ns.<br> <strong>Sampling rate:</strong> every 10 ps. <strong>Time integration step:</strong> 2 fs. <strong>Thermodynamic ensemble:</strong> NpT. <br> <strong>Temperature coupling:</strong> 'Berendsen' [<em>J. Chem. Phys.</em> <strong>81</strong> 3684 (1984)] with lipids and water coupled separately at T = 323 K.<br> <strong>Pressure coupling: '</strong>Berendsen' [<em>J. Chem. Phys.</em> <strong>81</strong> 3684 (1984)] with xy and z coupled separately at p = 1.0 bar. <strong>Electrostatics: </strong>PME [<em>J. Chem. Phys.</em> <strong>98</strong> 10089 (1993); <em>J. Chem. Phys.</em> <strong>103</strong> 8577 (1995)], real-space cutoff at 1.0 nm.<br> <strong>Van der Waals:</strong> Truncated at 1.0 nm. <strong>Constraints: </strong>Covalent bond lengths in lipids using LINCS [<em>J. Comput. Chem.</em> <strong>18</strong> 1463 (1997)], in water using SETTLE [J. Comput. Chem. <strong>13</strong> 952 (1992)]. <strong>Used in publications: </strong>[1] Markus S. Miettinen, Andrey A. Gurtovenko, Ilpo Vattulainen, and Mikko Karttunen: "Ion Dynamics in Cationic Lipid Bilayer Systems in Saline Solutions". <em>J. Phys. Chem. B</em> <strong>113</strong> 9226 (2009). DOI: 10.1021/jp810233q. [2] Markus S. Miettinen: "Computational Modeling of Cationic Lipid Bilayers in Saline Solutions". PhD Thesis. Aalto University School of Science and Technology, Helsinki, Finland. (2010). ISBN 978-952-60-3194-1.
DOI: 10.5281/zenodo.51639
title: Molecular dynamics simulation trajectory of a cationic lipid bilayer: 6/94 mol% DMTAP/DMPC

description: <strong>System: </strong>Symmetric bilayer of cationic DMTAP (dimyristoyltrimethylammoniumpropane, 6 mol-%) and zwitterionic DMPC (dimyristoylphosphatidylcholine, 94 mol-%) lipids in water. <strong>Number of DMPC: </strong>120.<br> <strong>Number of DMTAP:</strong> 8.<br> <strong>Number of Cl<sup>-</sup>-ions:</strong> 8.<br> <strong>Number of waters:</strong> 5099. <strong>Lipid model:</strong> 'Berger' united-atom [<em>Biophys. J.</em> <strong>72</strong> 2002 (1997)] with DMTAP modification by Gurtovenko et al. [<em>Biophys. J. </em><strong>86</strong> 3461 (2004)].<br> <strong>Water model:</strong> SPC [In <em>Intermolecular Forces,</em> ed. Pullman. 331 (1981)]. <strong>Simulation engine:</strong> Gromacs 3.x [www.gromacs.org] <strong>Trajectory length:</strong> 109 ns.<br> <strong>Previously equilibrated for:</strong> 32 ns.<br> <strong>Sampling rate:</strong> every 10 ps. <strong>Time integration step:</strong> 2 fs. <strong>Thermodynamic ensemble:</strong> NpT. <br> <strong>Temperature coupling:</strong> 'Berendsen' [<em>J. Chem. Phys.</em> <strong>81</strong> 3684 (1984)] with lipids and water coupled separately at T = 323 K.<br> <strong>Pressure coupling: '</strong>Berendsen' [<em>J. Chem. Phys.</em> <strong>81</strong> 3684 (1984)] with xy and z coupled separately at p = 1.0 bar. <strong>Electrostatics: </strong>PME [<em>J. Chem. Phys.</em> <strong>98</strong> 10089 (1993); <em>J. Chem. Phys.</em> <strong>103</strong> 8577 (1995)], real-space cutoff at 1.0 nm.<br> <strong>Van der Waals:</strong> Truncated at 1.0 nm. <strong>Constraints: </strong>Covalent bond lengths in lipids using LINCS [<em>J. Comput. Chem.</em> <strong>18</strong> 1463 (1997)], in water using SETTLE [J. Comput. Chem. <strong>13</strong> 952 (1992)]. <strong>Used in publications: </strong>[1] Markus S. Miettinen, Andrey A. Gurtovenko, Ilpo Vattulainen, and Mikko Karttunen: "Ion Dynamics in Cationic Lipid Bilayer Systems in Saline Solutions". <em>J. Phys. Chem. B</em> <strong>113</strong> 9226 (2009). DOI: 10.1021/jp810233q. [2] Markus S. Miettinen: "Computational Modeling of Cationic Lipid Bilayers in Saline Solutions". PhD Thesis. Aalto University School of Science and Technology, Helsinki, Finland. (2010). ISBN 978-952-60-3194-1.
DOI: 10.5281/zenodo.633761
title: Molecular dynamics simulation trajectory of a cationic lipid bilayer: 6/94 mol% DMTAP/DMPC

description: <strong>System: </strong>Symmetric bilayer of cationic DMTAP (dimyristoyltrimethylammoniumpropane, 6 mol-%) and zwitterionic DMPC (dimyristoylphosphatidylcholine, 94 mol-%) lipids in water. <strong>Number of DMPC: </strong>120.<br> <strong>Number of DMTAP:</strong> 8.<br> <strong>Number of Cl<sup>-</sup>-ions:</strong> 8.<br> <strong>Number of waters:</strong> 5099. <strong>Lipid model:</strong> 'Berger' united-atom [<em>Biophys. J.</em> <strong>72</strong> 2002 (1997)] with DMTAP modification by Gurtovenko et al. [<em>Biophys. J. </em><strong>86</strong> 3461 (2004)].<br> <strong>Water model:</strong> SPC [In <em>Intermolecular Forces,</em> ed. Pullman. 331 (1981)]. <strong>Simulation engine:</strong> Gromacs 3.x [www.gromacs.org] <strong>Trajectory length:</strong> 109 ns.<br> <strong>Previously equilibrated for:</strong> 32 ns.<br> <strong>Sampling rate:</strong> every 10 ps. <strong>Time integration step:</strong> 2 fs. <strong>Thermodynamic ensemble:</strong> NpT. <br> <strong>Temperature coupling:</strong> 'Berendsen' [<em>J. Chem. Phys.</em> <strong>81</strong> 3684 (1984)] with lipids and water coupled separately at T = 323 K.<br> <strong>Pressure coupling: '</strong>Berendsen' [<em>J. Chem. Phys.</em> <strong>81</strong> 3684 (1984)] with xy and z coupled separately at p = 1.0 bar. <strong>Electrostatics: </strong>PME [<em>J. Chem. Phys.</em> <strong>98</strong> 10089 (1993); <em>J. Chem. Phys.</em> <strong>103</strong> 8577 (1995)], real-space cutoff at 1.0 nm.<br> <strong>Van der Waals:</strong> Truncated at 1.0 nm. <strong>Constraints: </strong>Covalent bond lengths in lipids using LINCS [<em>J. Comput. Chem.</em> <strong>18</strong> 1463 (1997)], in water using SETTLE [J. Comput. Chem. <strong>13</strong> 952 (1992)]. <strong>Used in publications: </strong>[1] Markus S. Miettinen, Andrey A. Gurtovenko, Ilpo Vattulainen, and Mikko Karttunen: "Ion Dynamics in Cationic Lipid Bilayer Systems in Saline Solutions". <em>J. Phys. Chem. B</em> <strong>113</strong> 9226 (2009). DOI: 10.1021/jp810233q. [2] Markus S. Miettinen: "Computational Modeling of Cationic Lipid Bilayers in Saline Solutions". PhD Thesis. Aalto University School of Science and Technology, Helsinki, Finland. (2010). ISBN 978-952-60-3194-1.
DOI: 10.5281/zenodo.51750
title: Molecular dynamics simulation trajectory of a cationic lipid bilayer: 75/25 mol% DMTAP/DMPC in 1.0 M NaCl

description: <strong>System: </strong>Symmetric bilayer of cationic DMTAP (dimyristoyltrimethylammoniumpropane, 75 mol-%) and zwitterionic DMPC (dimyristoylphosphatidylcholine, 25 mol-%) lipids in 1.0 M NaCl solution. <strong>Number of DMPC:</strong> 32.<br> <strong>Number of DMTAP:</strong> 96.<br> <strong>Number of Na<sup>+</sup>-ions:</strong> 96.<br> <strong>Number of Cl<sup>-</sup>-ions:</strong> 192.<br> <strong>Number of waters:</strong> 5304. <strong>Lipid model:</strong> 'Berger' united-atom [<em>Biophys. J.</em> <strong>72</strong> 2002 (1997)] with DMTAP modification by Gurtovenko et al. [<em>Biophys. J. </em><strong>86</strong> 3461 (2004)].<br> <strong>Water model:</strong> SPC [In <em>Intermolecular Forces,</em> ed. Pullman. 331 (1981)]. <strong>Simulation engine:</strong> Gromacs 3.x [www.gromacs.org] <strong>Trajectory length:</strong> 110 ns.<br> <strong>Previously equilibrated for:</strong> 11 ns.<br> <strong>Sampling rate:</strong> every 10 ps. <strong>Time integration step:</strong> 2 fs. <strong>Thermodynamic ensemble:</strong> NpT. <br> <strong>Temperature coupling:</strong> 'Berendsen' [<em>J. Chem. Phys.</em> <strong>81</strong> 3684 (1984)] with lipids and water coupled separately at T = 323 K.<br> <strong>Pressure coupling: '</strong>Berendsen' [<em>J. Chem. Phys.</em> <strong>81</strong> 3684 (1984)] with xy and z coupled separately at p = 1.0 bar. <strong>Electrostatics: </strong>PME [<em>J. Chem. Phys.</em> <strong>98</strong> 10089 (1993); <em>J. Chem. Phys.</em> <strong>103</strong> 8577 (1995)], real-space cutoff at 1.0 nm.<br> <strong>Van der Waals:</strong> Truncated at 1.0 nm. <strong>Constraints: </strong>Covalent bond lengths in lipids using LINCS [<em>J. Comput. Chem.</em> <strong>18</strong> 1463 (1997)], in water using SETTLE [J. Comput. Chem. <strong>13</strong> 952 (1992)]. <strong>Used in publications: </strong>[1] Markus S. Miettinen, Andrey A. Gurtovenko, Ilpo Vattulainen, and Mikko Karttunen: "Ion Dynamics in Cationic Lipid Bilayer Systems in Saline Solutions". <em>J. Phys. Chem. B</em> <strong>113</strong> 9226 (2009). DOI: 10.1021/jp810233q. [2] Markus S. Miettinen: "Computational Modeling of Cationic Lipid Bilayers in Saline Solutions". PhD Thesis. Aalto University School of Science and Technology, Helsinki, Finland. (2010). ISBN 978-952-60-3194-1.
DOI: 10.5281/zenodo.633762
title: Molecular dynamics simulation trajectory of a cationic lipid bilayer: 75/25 mol% DMTAP/DMPC in 1.0 M NaCl

description: <strong>System: </strong>Symmetric bilayer of cationic DMTAP (dimyristoyltrimethylammoniumpropane, 75 mol-%) and zwitterionic DMPC (dimyristoylphosphatidylcholine, 25 mol-%) lipids in 1.0 M NaCl solution. <strong>Number of DMPC:</strong> 32.<br> <strong>Number of DMTAP:</strong> 96.<br> <strong>Number of Na<sup>+</sup>-ions:</strong> 96.<br> <strong>Number of Cl<sup>-</sup>-ions:</strong> 192.<br> <strong>Number of waters:</strong> 5304. <strong>Lipid model:</strong> 'Berger' united-atom [<em>Biophys. J.</em> <strong>72</strong> 2002 (1997)] with DMTAP modification by Gurtovenko et al. [<em>Biophys. J. </em><strong>86</strong> 3461 (2004)].<br> <strong>Water model:</strong> SPC [In <em>Intermolecular Forces,</em> ed. Pullman. 331 (1981)]. <strong>Simulation engine:</strong> Gromacs 3.x [www.gromacs.org] <strong>Trajectory length:</strong> 110 ns.<br> <strong>Previously equilibrated for:</strong> 11 ns.<br> <strong>Sampling rate:</strong> every 10 ps. <strong>Time integration step:</strong> 2 fs. <strong>Thermodynamic ensemble:</strong> NpT. <br> <strong>Temperature coupling:</strong> 'Berendsen' [<em>J. Chem. Phys.</em> <strong>81</strong> 3684 (1984)] with lipids and water coupled separately at T = 323 K.<br> <strong>Pressure coupling: '</strong>Berendsen' [<em>J. Chem. Phys.</em> <strong>81</strong> 3684 (1984)] with xy and z coupled separately at p = 1.0 bar. <strong>Electrostatics: </strong>PME [<em>J. Chem. Phys.</em> <strong>98</strong> 10089 (1993); <em>J. Chem. Phys.</em> <strong>103</strong> 8577 (1995)], real-space cutoff at 1.0 nm.<br> <strong>Van der Waals:</strong> Truncated at 1.0 nm. <strong>Constraints: </strong>Covalent bond lengths in lipids using LINCS [<em>J. Comput. Chem.</em> <strong>18</strong> 1463 (1997)], in water using SETTLE [J. Comput. Chem. <strong>13</strong> 952 (1992)]. <strong>Used in publications: </strong>[1] Markus S. Miettinen, Andrey A. Gurtovenko, Ilpo Vattulainen, and Mikko Karttunen: "Ion Dynamics in Cationic Lipid Bilayer Systems in Saline Solutions". <em>J. Phys. Chem. B</em> <strong>113</strong> 9226 (2009). DOI: 10.1021/jp810233q. [2] Markus S. Miettinen: "Computational Modeling of Cationic Lipid Bilayers in Saline Solutions". PhD Thesis. Aalto University School of Science and Technology, Helsinki, Finland. (2010). ISBN 978-952-60-3194-1.
DOI: 10.5281/zenodo.51754
title: Molecular dynamics simulation trajectory of a cationic lipid bilayer: 75/25 mol% DMTAP/DMPC in 0.5 M NaCl

description: <strong>System: </strong>Symmetric bilayer of cationic DMTAP (dimyristoyltrimethylammoniumpropane, 75 mol-%) and zwitterionic DMPC (dimyristoylphosphatidylcholine, 25 mol-%) lipids in 0.5 M NaCl solution. <strong>Number of DMPC:</strong> 32.<br> <strong>Number of DMTAP:</strong> 96.<br> <strong>Number of Na<sup>+</sup>-ions:</strong> 49.<br> <strong>Number of Cl<sup>-</sup>-ions:</strong> 145.<br> <strong>Number of waters:</strong> 5398. <strong>Lipid model:</strong> 'Berger' united-atom [<em>Biophys. J.</em> <strong>72</strong> 2002 (1997)] with DMTAP modification by Gurtovenko et al. [<em>Biophys. J. </em><strong>86</strong> 3461 (2004)].<br> <strong>Water model:</strong> SPC [In <em>Intermolecular Forces,</em> ed. Pullman. 331 (1981)]. <strong>Simulation engine:</strong> Gromacs 3.x [www.gromacs.org] <strong>Trajectory length:</strong> 110 ns.<br> <strong>Previously equilibrated for:</strong> 11 ns.<br> <strong>Sampling rate:</strong> every 10 ps. <strong>Time integration step:</strong> 2 fs. <strong>Thermodynamic ensemble:</strong> NpT. <br> <strong>Temperature coupling:</strong> 'Berendsen' [<em>J. Chem. Phys.</em> <strong>81</strong> 3684 (1984)] with lipids and water coupled separately at T = 323 K.<br> <strong>Pressure coupling: '</strong>Berendsen' [<em>J. Chem. Phys.</em> <strong>81</strong> 3684 (1984)] with xy and z coupled separately at p = 1.0 bar. <strong>Electrostatics: </strong>PME [<em>J. Chem. Phys.</em> <strong>98</strong> 10089 (1993); <em>J. Chem. Phys.</em> <strong>103</strong> 8577 (1995)], real-space cutoff at 1.0 nm.<br> <strong>Van der Waals:</strong> Truncated at 1.0 nm. <strong>Constraints: </strong>Covalent bond lengths in lipids using LINCS [<em>J. Comput. Chem.</em> <strong>18</strong> 1463 (1997)], in water using SETTLE [J. Comput. Chem. <strong>13</strong> 952 (1992)]. <strong>Used in publications: </strong>[1] Markus S. Miettinen, Andrey A. Gurtovenko, Ilpo Vattulainen, and Mikko Karttunen: "Ion Dynamics in Cationic Lipid Bilayer Systems in Saline Solutions". <em>J. Phys. Chem. B</em> <strong>113</strong> 9226 (2009). DOI: 10.1021/jp810233q. [2] Markus S. Miettinen: "Computational Modeling of Cationic Lipid Bilayers in Saline Solutions". PhD Thesis. Aalto University School of Science and Technology, Helsinki, Finland. (2010). ISBN 978-952-60-3194-1.
DOI: 10.5281/zenodo.633766
title: Molecular dynamics simulation trajectory of a cationic lipid bilayer: 75/25 mol% DMTAP/DMPC in 0.5 M NaCl

description: <strong>System: </strong>Symmetric bilayer of cationic DMTAP (dimyristoyltrimethylammoniumpropane, 75 mol-%) and zwitterionic DMPC (dimyristoylphosphatidylcholine, 25 mol-%) lipids in 0.5 M NaCl solution. <strong>Number of DMPC:</strong> 32.<br> <strong>Number of DMTAP:</strong> 96.<br> <strong>Number of Na<sup>+</sup>-ions:</strong> 49.<br> <strong>Number of Cl<sup>-</sup>-ions:</strong> 145.<br> <strong>Number of waters:</strong> 5398. <strong>Lipid model:</strong> 'Berger' united-atom [<em>Biophys. J.</em> <strong>72</strong> 2002 (1997)] with DMTAP modification by Gurtovenko et al. [<em>Biophys. J. </em><strong>86</strong> 3461 (2004)].<br> <strong>Water model:</strong> SPC [In <em>Intermolecular Forces,</em> ed. Pullman. 331 (1981)]. <strong>Simulation engine:</strong> Gromacs 3.x [www.gromacs.org] <strong>Trajectory length:</strong> 110 ns.<br> <strong>Previously equilibrated for:</strong> 11 ns.<br> <strong>Sampling rate:</strong> every 10 ps. <strong>Time integration step:</strong> 2 fs. <strong>Thermodynamic ensemble:</strong> NpT. <br> <strong>Temperature coupling:</strong> 'Berendsen' [<em>J. Chem. Phys.</em> <strong>81</strong> 3684 (1984)] with lipids and water coupled separately at T = 323 K.<br> <strong>Pressure coupling: '</strong>Berendsen' [<em>J. Chem. Phys.</em> <strong>81</strong> 3684 (1984)] with xy and z coupled separately at p = 1.0 bar. <strong>Electrostatics: </strong>PME [<em>J. Chem. Phys.</em> <strong>98</strong> 10089 (1993); <em>J. Chem. Phys.</em> <strong>103</strong> 8577 (1995)], real-space cutoff at 1.0 nm.<br> <strong>Van der Waals:</strong> Truncated at 1.0 nm. <strong>Constraints: </strong>Covalent bond lengths in lipids using LINCS [<em>J. Comput. Chem.</em> <strong>18</strong> 1463 (1997)], in water using SETTLE [J. Comput. Chem. <strong>13</strong> 952 (1992)]. <strong>Used in publications: </strong>[1] Markus S. Miettinen, Andrey A. Gurtovenko, Ilpo Vattulainen, and Mikko Karttunen: "Ion Dynamics in Cationic Lipid Bilayer Systems in Saline Solutions". <em>J. Phys. Chem. B</em> <strong>113</strong> 9226 (2009). DOI: 10.1021/jp810233q. [2] Markus S. Miettinen: "Computational Modeling of Cationic Lipid Bilayers in Saline Solutions". PhD Thesis. Aalto University School of Science and Technology, Helsinki, Finland. (2010). ISBN 978-952-60-3194-1.
DOI: 10.5281/zenodo.51748
title: Molecular dynamics simulation trajectory of a cationic lipid bilayer: 50/50 mol% DMTAP/DMPC

description: <strong>System: </strong>Symmetric bilayer of cationic DMTAP (dimyristoyltrimethylammoniumpropane, 50 mol-%) and zwitterionic DMPC (dimyristoylphosphatidylcholine, 50 mol-%) lipids in water. <strong>Number of DMPC: </strong>64.<br> <strong>Number of DMTAP:</strong> 64.<br> <strong>Number of Cl--ions:</strong> 64.<br> <strong>Number of waters:</strong> 5336. <strong>Lipid model:</strong> 'Berger' united-atom [<em>Biophys. J.</em> <strong>72</strong> 2002 (1997)] with DMTAP modification by Gurtovenko et al. [<em>Biophys. J. </em><strong>86</strong> 3461 (2004)].<br> <strong>Water model:</strong> SPC [In <em>Intermolecular Forces,</em> ed. Pullman. 331 (1981)]. <strong>Simulation engine:</strong> Gromacs 3.x [www.gromacs.org] <strong>Trajectory length:</strong> 149 ns.<br> <strong>Previously equilibrated for:</strong> 41 ns.<br> <strong>Sampling rate:</strong> every 10 ps. <strong>Time integration step:</strong> 2 fs. <strong>Thermodynamic ensemble:</strong> NpT. <br> <strong>Temperature coupling:</strong> 'Berendsen' [<em>J. Chem. Phys.</em> <strong>81</strong> 3684 (1984)] with lipids and water coupled separately at T = 323 K.<br> <strong>Pressure coupling: '</strong>Berendsen' [<em>J. Chem. Phys.</em> <strong>81</strong> 3684 (1984)] with xy and z coupled separately at p = 1.0 bar. <strong>Electrostatics: </strong>PME [<em>J. Chem. Phys.</em> <strong>98</strong> 10089 (1993); <em>J. Chem. Phys.</em> <strong>103</strong> 8577 (1995)], real-space cutoff at 1.0 nm.<br> <strong>Van der Waals:</strong> Truncated at 1.0 nm. <strong>Constraints: </strong>Covalent bond lengths in lipids using LINCS [<em>J. Comput. Chem.</em> <strong>18</strong> 1463 (1997)], in water using SETTLE [J. Comput. Chem. <strong>13</strong> 952 (1992)]. <strong>Used in publications: </strong>[1] Markus S. Miettinen, Andrey A. Gurtovenko, Ilpo Vattulainen, and Mikko Karttunen: "Ion Dynamics in Cationic Lipid Bilayer Systems in Saline Solutions". <em>J. Phys. Chem. B</em> <strong>113</strong> 9226 (2009). DOI: 10.1021/jp810233q. [2] Markus S. Miettinen: "Computational Modeling of Cationic Lipid Bilayers in Saline Solutions". PhD Thesis. Aalto University School of Science and Technology, Helsinki, Finland. (2010). ISBN 978-952-60-3194-1.
DOI: 10.5281/zenodo.633770
title: Molecular dynamics simulation trajectory of a cationic lipid bilayer: 50/50 mol% DMTAP/DMPC

description: <strong>System: </strong>Symmetric bilayer of cationic DMTAP (dimyristoyltrimethylammoniumpropane, 50 mol-%) and zwitterionic DMPC (dimyristoylphosphatidylcholine, 50 mol-%) lipids in water. <strong>Number of DMPC: </strong>64.<br> <strong>Number of DMTAP:</strong> 64.<br> <strong>Number of Cl--ions:</strong> 64.<br> <strong>Number of waters:</strong> 5336. <strong>Lipid model:</strong> 'Berger' united-atom [<em>Biophys. J.</em> <strong>72</strong> 2002 (1997)] with DMTAP modification by Gurtovenko et al. [<em>Biophys. J. </em><strong>86</strong> 3461 (2004)].<br> <strong>Water model:</strong> SPC [In <em>Intermolecular Forces,</em> ed. Pullman. 331 (1981)]. <strong>Simulation engine:</strong> Gromacs 3.x [www.gromacs.org] <strong>Trajectory length:</strong> 149 ns.<br> <strong>Previously equilibrated for:</strong> 41 ns.<br> <strong>Sampling rate:</strong> every 10 ps. <strong>Time integration step:</strong> 2 fs. <strong>Thermodynamic ensemble:</strong> NpT. <br> <strong>Temperature coupling:</strong> 'Berendsen' [<em>J. Chem. Phys.</em> <strong>81</strong> 3684 (1984)] with lipids and water coupled separately at T = 323 K.<br> <strong>Pressure coupling: '</strong>Berendsen' [<em>J. Chem. Phys.</em> <strong>81</strong> 3684 (1984)] with xy and z coupled separately at p = 1.0 bar. <strong>Electrostatics: </strong>PME [<em>J. Chem. Phys.</em> <strong>98</strong> 10089 (1993); <em>J. Chem. Phys.</em> <strong>103</strong> 8577 (1995)], real-space cutoff at 1.0 nm.<br> <strong>Van der Waals:</strong> Truncated at 1.0 nm. <strong>Constraints: </strong>Covalent bond lengths in lipids using LINCS [<em>J. Comput. Chem.</em> <strong>18</strong> 1463 (1997)], in water using SETTLE [J. Comput. Chem. <strong>13</strong> 952 (1992)]. <strong>Used in publications: </strong>[1] Markus S. Miettinen, Andrey A. Gurtovenko, Ilpo Vattulainen, and Mikko Karttunen: "Ion Dynamics in Cationic Lipid Bilayer Systems in Saline Solutions". <em>J. Phys. Chem. B</em> <strong>113</strong> 9226 (2009). DOI: 10.1021/jp810233q. [2] Markus S. Miettinen: "Computational Modeling of Cationic Lipid Bilayers in Saline Solutions". PhD Thesis. Aalto University School of Science and Technology, Helsinki, Finland. (2010). ISBN 978-952-60-3194-1.
DOI: 10.5519/qd.zmpae5b7
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (51913 records)
DOI: 10.5281/zenodo.53222
title: Molecular dynamics simulation trajectory of a cationic lipid bilayer: 6/94 mol% DMTAP/DMPC in 1.0 M NaCl

description: <strong>System: </strong>Symmetric bilayer of cationic DMTAP (dimyristoyltrimethylammoniumpropane, 6 mol-%) and zwitterionic DMPC (dimyristoylphosphatidylcholine, 94 mol-%) lipids in 1.0 M NaCl solution. <strong>Number of DMPC:</strong> 120.<br> <strong>Number of DMTAP:</strong> 8.<br> <strong>Number of Na<sup>+</sup>-ions:</strong> 89.<br> <strong>Number of Cl<sup>-</sup>-ions:</strong> 97.<br> <strong>Number of waters:</strong> 4921. <strong>Lipid model:</strong> 'Berger' united-atom [<em>Biophys. J.</em> <strong>72</strong> 2002 (1997)] with DMTAP modification by Gurtovenko et al. [<em>Biophys. J. </em><strong>86</strong> 3461 (2004)].<br> <strong>Water model:</strong> SPC [In <em>Intermolecular Forces,</em> ed. Pullman. 331 (1981)]. <strong>Simulation engine:</strong> Gromacs 3.x [www.gromacs.org] <strong>Trajectory length:</strong> 230 ns.<br> <strong>Previously equilibrated for:</strong> 12 ns.<br> <strong>Sampling rate:</strong> every 10 ps. <strong>Time integration step:</strong> 2 fs. <strong>Thermodynamic ensemble:</strong> NpT. <br> <strong>Temperature coupling:</strong> 'Berendsen' [<em>J. Chem. Phys.</em> <strong>81</strong> 3684 (1984)] with lipids and water coupled separately at T = 323 K.<br> <strong>Pressure coupling: '</strong>Berendsen' [<em>J. Chem. Phys.</em> <strong>81</strong> 3684 (1984)] with xy and z coupled separately at p = 1.0 bar. <strong>Electrostatics: </strong>PME [<em>J. Chem. Phys.</em> <strong>98</strong> 10089 (1993); <em>J. Chem. Phys.</em> <strong>103</strong> 8577 (1995)], real-space cutoff at 1.0 nm.<br> <strong>Van der Waals:</strong> Truncated at 1.0 nm. <strong>Constraints: </strong>Covalent bond lengths in lipids using LINCS [<em>J. Comput. Chem.</em> <strong>18</strong> 1463 (1997)], in water using SETTLE [J. Comput. Chem. <strong>13</strong> 952 (1992)]. <strong>Used in publications: </strong>[1] Markus S. Miettinen, Andrey A. Gurtovenko, Ilpo Vattulainen, and Mikko Karttunen: "Ion Dynamics in Cationic Lipid Bilayer Systems in Saline Solutions". <em>J. Phys. Chem. B</em> <strong>113</strong> 9226 (2009). DOI: 10.1021/jp810233q. [2] Markus S. Miettinen: "Computational Modeling of Cationic Lipid Bilayers in Saline Solutions". PhD Thesis. Aalto University School of Science and Technology, Helsinki, Finland. (2010). ISBN 978-952-60-3194-1.