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17 results for “DMPC”
Configurations and parameters for DMPC and DMTAP lipids and their mixtures
<p><strong>Configurations</strong> containing cationic (charge: +1) DMTAP and DMPC lipids, water and neutralizing ions (when necessary) at 50 C for the following systems:</p> <ol> <li>Pure DMPC: 128 lipids (all DMPC, 0 Cl ions) and 3655 waters. File: dmpc128_20ns.pdb</li> <li>6% DMTAP: 128 lipids (120 DMPC, 8 DMTAP, 8 Cl ions) and 3647 waters. File: tap06_20ns.pdb</li> <li>16% DMTAP: 128 lipids (108 DMPC, 20 DMTAP, 20 Cl ions) and 3635 waters</li> <li>25% DMTAP: 128 lipids (96 DMPC, 32 DMTAP, 32 Cl ions) and 3623 waters</li> <li>31% DMTAP: 128 lipids (88 DMPC, 40 DMTAP, 40 Cl ions) and 3615 waters</li> <li>39% DMTAP: 128 lipids (78 DMPC, 50 DMTAP, 50 Cl ions) and 3605 waters</li> <li>50% DMTAP: 128 lipids (64 DMPC, 64 DMTAP, 64 Cl ions) and 3591 waters</li> <li>63% DMTAP: 128 lipids (48 DMPC, 80 DMTAP, 80 Cl ions) and 3575 waters</li> <li>75% DMTAP: 128 lipids (32 DMPC, 96 DMTAP, 96 Cl ions) and 3559 waters</li> <li>89% DMTAP: 128 lipids (14 DMPC, 114 DMTAP, 114 Cl ions) and 3541 waters</li> <li>Pure DMTAP: 128 lipids (all DMTAP, 128 Cl ions) and 3527 waters: File: dmtap128_24ns.pdb</li> </ol> <p>Simulation time for each system is shown in the file name.</p> <p><strong>Parameter files are: </strong>dmpc.itp and dmtap.itp. The file lipid.itp is also needed (these are Berger lipids). Download lipid.itp from <a href="http://wcm.ucalgary.ca/tieleman/downloads">http://wcm.ucalgary.ca/tieleman/downloads</a></p> <p><strong>The PDF file</strong> (TablePDB.pdf ) contains a summary of the systems with area per lipid and error.</p> <p><strong>References:</strong></p> <ol> <li><a href="http://www.biophysj.org/cgi/content/abstract/86/6/3461">Cationic DMPC/DMTAP Lipid Bilayers: Molecular Dynamics Study</a>, Gurtovenko, Patra, Karttunen, Vattulainen, Biophys. J. 86, 3461-3472 (2004).</li> <li><a href="http://dx.doi.org/10.1021/jp053667m">Effect of Monovalent Salt on Cationic Lipid Membranes As Revealed by Molecular Dynamics Simulations</a>, A. A. Gurtovenko, M. Miettinen, M. Karttunen, and I. Vattulainen J. Phys. Chem. B 109, 21126-21134 (2005).</li> <li><a href="http://dx.doi.org/10.1021/jp810233q">Ion Dynamics in Cationic Lipid Bilayer Systems in Saline Solutions</a>, M.S. Miettinen, A.A. Gurtovenko, I. Vattulainen, and M. Karttunen, J. Phys. Chem. B 113, 9226-9234 (2009).</li> </ol> <p> </p> <p> </p>
MD simulations of bOG:DMPC in CHARMM36 force field
<p>CHARMM-GUI based series of simulations of beta-octyl-D-glucopyranoside (b-OG) mixed with DMPC at different dilutions. bOG:DMPC mol ratios are 1:1, 1:2, and 2:3. The only change in the force field was changing atom names from 2H2 to H2 in BOG residue to allow **gmx grompp** to recognize protons as protons when setting up constraints for bonds with hydrogens.</p> <p>Simulations are performed in highly hydrated state. I can name it "more than 50 water per two acyl chains"; "water per lipid" measure doesn't work here because bOG has just a single hydrocarbon tail.</p> <p>Trajectory length: 500 ns (20 ps step). T = 303 K. </p> <p>In this version we add *znd files where atom names are unique (changed in a new version of BOG.itp).</p>
MD simulation trajectory and related files for DMPC bilayer, Högberg et al, J.Comp.Chem., 29, 2359 (2008)
<p>MD simulation trajectory and related files for DMPC bilayer, from paper: C.J.Högberg, A.M,Nikitin, A.P.Lyubartsev, J.Comp.Chem., 29, 2359 (2008)</p> <p>25ns( excluded) + 55 ns trajectory<br /> T=303K, 98 lipids + 2700 H2O<br /> software: MDynaMix v 5.0</p> <p>Relevant files:</p> <p>md.input : main MD input file</p> <p>dmpc_2008.mmol : lipid topology/force field file<br /> H2O.mmol : SPC water</p> <p>order.in : Input for the analysis utility to extract order parameters</p> <p>Trajectory files:</p> <p>dmpc_NewMod.250 - dmpc_NewMod.849</p> <p>Most of files contain 100 frames taken with 1 ps interval</p>
Molecular dynamics simulation trajectory of a fully hydrated DMPC lipid bilayer
<p><strong>System: </strong>DMPC (dimyristoylphosphatidylcholine) bilayer in water.</p> <p><strong>Number of lipids: </strong>128.<br> <strong>Number of waters:</strong> 5097.</p> <p><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)].</p> <p><strong>Simulation engine:</strong> Gromacs 3.x [www.gromacs.org]</p> <p><strong>Trajectory length:</strong> 110 ns.<br> <strong>Previously equilibrated for:</strong> 20 ns.<br> <strong>Sampling rate:</strong> every 10 ps.</p> <p><strong>Time integration step:</strong> 2 fs.</p> <p><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.</p> <p><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.</p> <p><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)].</p> <p><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.</p>
200 ns simulation of a DMPC bilayer using Gromos 53A6 + Berger lipids
<p><strong>MD simulation of a DMPC bilayer: 200 ns </strong></p> <ul> <li>Gromos 53A6 force field and Berger lipids (lipid.itp)</li> <li>128 DMPC lipids and 3655 SPC waters. Total number of atoms: 16853.</li> <li>This simulation: 200 ns. The systems was equilibrated for 52 ns before this run.</li> <li>Simulation details: <ul> <li>Temperature: 323 K</li> <li>Times step: 2 fs</li> <li>V-rescale thermostat, Parrinello-Rahman barostat, P-LINCS for constraints</li> <li>The run was done using a laptop with GTX980M. Performance: ~105ns/day</li> </ul> </li> <li>Area per lipid and thickness (P-P distance) are provided.</li> </ul>
OpenMM simulations of DMPC using the CHARMM Drude2023 force field
<p>The dataset contains a PSF, a formatted coordinate file (CRD), and DCD files with the final 200 ns from<br> each of 3 replicate simulations from the paper</p> <p><br> <strong>Drude Polarizable Lipid Force Field with Explicit Treatment of LongRange Dispersion:<br> Parametrization and Validation for Saturated and Monounsaturated Zwitterionic Lipids</strong><br> Yalun Yu, Richard M. Venable, Jonathan Thirman, Payal Chatterjee, Anmol Kumar, Richard W. Pastor,*<br> Benoît Roux,* Alexander D. MacKerell, Jr.,* and Jeffery B. Klauda*<br> https://doi.org/10.1021/acs.jctc.3c00203</p> <p>DCD file names indicate the lipid, replica number, and the time point of the final coordinate set in the file Each file has 50 ns of data, with coordinate sets spaced at 10 ps between frames.</p>
All-atomic simulation of DMPC bilayer with PME and with RFZ
<p>We have performed simulations of DMPC to check if the <strong>reaction-field-zero</strong> mode of calculating electrostatics is a good substitute for PME if we want to avoid PME for some reasons (e.g. for stress calculations). We started this simulation from the configuration deposited by Matti Javanainen (10.5281/zenodo.6943413). We performed two simulations of about 500 ns with the same protocol but at 313 K. Protocol for reaction-field-zero is supplemented as well. POPE simulated with the same RFZ protocol is deposited in a separate dataset (10.5281/zenodo.8435138).</p>
MD simulation of DMPC bilayer with CHARMM36 force field. 20 w/l
<p>MD simulation of DMPC bilayer with CHARMM36 force field. 20 w/l.</p> <p>Dataset contains simulation files including trajectories (.xtc) (original production.xtc, and equilibrated and centered centered_pbcmol-20-500ns.xtc).</p> <p>System: DMPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 4000</p> <p>Simulation time: 500 ns</p> <p>Simulation engine: GROMACS 2019.5</p> <p>Temperature: 314 K</p>
MD simulation of DMPC bilayer with CHARMM36 force field. 10 w/l.
<p>MD simulation of DMPC bilayer with CHARMM36 force field. 10 w/l.</p> <p>Dataset contains simulation files including trajectories (.xtc) (original production.xtc, and equilibrated and centered centered_pbcmol-50-500ns.xtc).</p> <p>System: DMPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 2000</p> <p>Simulation time: 500 ns</p> <p>Simulation engine: GROMACS 2019.5</p> <p>Temperature: 314 K</p>
MD simulation of DMPC bilayer with CHARMM36 force field. Full hydration
<p>MD simulation of DMPC bilayer with CHARMM36 force field. Full hydration</p> <p>Dataset contains simulation files including trajectories (.xtc) (original production.xtc, and equilibrated and centered ).</p> <p>System: DMPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 10000</p> <p>Simulation time: 500 ns</p> <p>Sampling rate: every 10 ps</p> <p>Simulation engine: GROMACS 2019.5</p> <p>Temperature: 314 K</p>
MD simulation of DMPC bilayer with CHARMM36 force field. 5 w/l.
<p>MD simulation of DMPC bilayer with CHARMM36 force field. 5 w/l.</p> <p>Dataset contains simulation files including trajectories (.xtc) (original production.xtc, and equilibrated and centered centered_pbcmol-20-500ns.xtc).</p> <p>System: DMPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 1000</p> <p>Simulation time: 1000 ns</p> <p>Simulation engine: GROMACS 2019.5</p> <p>Temperature: 314 K</p>
OpenMM simulations of DMPC using the CHARMM Drude2023 force field in xtc format
<p>The dataset contains a PSF, a formatted coordinate file (CRD), and XTC files with the final 200 ns from<br> each of 3 replicate simulations from the paper</p> <p><br> <strong>Drude Polarizable Lipid Force Field with Explicit Treatment of LongRange Dispersion:<br> Parametrization and Validation for Saturated and Monounsaturated Zwitterionic Lipids</strong><br> Yalun Yu, Richard M. Venable, Jonathan Thirman, Payal Chatterjee, Anmol Kumar, Richard W. Pastor,*<br> Benoît Roux,* Alexander D. MacKerell, Jr.,* and Jeffery B. Klauda*<br> https://doi.org/10.1021/acs.jctc.3c00203</p> <p>XTC file names indicate the lipid and the replica number; each file has frames spaced at 10 ps over a 200 ns interval.</p> <p>The DCD sub-files in <span>10.5281/zenodo.7872767</span> have been concatenated into a single 200 ns long trajectory in xtc format by Batuhan Kav using MDAnalysis.</p>
MD simulation of DMPC bilayer with OPLS4 force field. 5 w/l.
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MD simulation of DMPC bilayer with OPLS4 force field. 10 w/l.
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MD simulation of DMPC bilayer with OPLS4 force field. 20 w/l.
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MD simulation of DMPC bilayer with OPLS4 force field. Full hydration.
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Simulations of a DMPC membrane with embedded cholesterol or rhodopsin
<p>Contain either 1 rhodopsin protein or 2 cholesterol molecules (1 per leaflet). 500 ns.</p> <p>Simulation at either 310 K (when explicitly mentioned) or 298 K (when not explicitly mentioned).</p> <p>The simulations at 298 K are in the ripple/gel phase.</p>
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