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158 results for “Charmm36”
Large DPPC monolayer simulations with Charmm36+OPC @ 298 K (Part 1/2)
<p>DPPC monolayers simulated at a varying area per lipid in the NVT ensemble. The Charmm36 lipid model [1] is employed together with the 4-point OPC water model [2]. Each system contains two monolayers with 256 lipids each. These monolayers are separated by a water slab, and surrounded by vacuum. </p> <p>The number in the filename corresponds to the area per lipid in Ångströms. The starting structures were generated by setting up a POPC monolayer system with an area per lipid of 50 Å^2, followed by a simulation during which the monolayer area was expanded using PLUMED. Next, POPC was replaced by DPPC, and the systems were energy minimized. Systems with area smaller than 51 Å^2 were generated by compressing the DPPC monolayer system with PLUMED.</p> <p>All trajectories, 100–200 ns long (until convergence of surface tension), are simulated with Gromacs 5.0.x [3] using the default Charmm36 monolayer simulations parameters given in the mdp file. Topology (.top) and index files are also common for all simulations. The topologies (.itp) for the lipids can be obtained from Charmm-GUI and for the OPC water model from https://bioinformatics.cs.vt.edu/~izadi/ .</p> <p>Part 2 of this upload is available at https://doi.org/10.5281/zenodo.838635</p> <p>Matti Javanainen, Antti Lamberg, Lukasz Cwiklik, Ilpo Vattulainen, and O. H. Samuli Ollila. <em>Atomistic Model for Nearly Quantitative Simulations of Langmuir Monolayers</em>, Langmuir <strong>2018</strong> 34 (7), 2565-2572, DOI: 10.1021/acs.langmuir.7b02855</p> <p>[1] DOI: 10.1021/jp101759q<br> [2] DOI: 10.1021/jz501780a<br> [3] DOI: 10.1016/j.softx.2015.06.001</p>
Simulations of large POPC bilayers using the Charmm36 force field.
<p>An earlier simulation (DOI:10.5281/zenodo.159759) of a POPC bilayer consisting of 200 lipids (100 per leaflet) is extended to 4 and 9 times larger (800 and 1800 lipids) and simulated for 100 ns using Gromacs v5.1.x [1]. The Charmm36 model [2] is employed for lipids and the Charmm-compatible variant of the tip3p model for water.</p> <p>The Charmm36 force field parameters were obtained from CHARMM-GUI [3] at http://www.charmm-gui.org</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>The files are in GROMACS format. The number in the file name corresponds to how many times larger the system is compared to that in (DOI:10.5281/zenodo.159759), either 4 (2x2) or 9 (3x3). Trajectories (.xtc) is 100 ns long with data saved every 100 ps. Additionally, the topology (.top), binary run input file for GROMACS v. 5.0–> (.tpr), the continue point file (.cpt), and the energy output file (.edr) are provided. The provided simulation paremeter file (.mdp) is common for both simulations. </p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>[1] GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. Mark J. Abraham, Teemu Murtola, Roland Schulz, Szilárd Páll, Jeremy C. Smith, Berk Hess, and Erik Lindahl. SoftwareX 2015 1–2, 19–25, DOI: 10.1016/j.softx.2015.06.001</p> <p>[2] Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types. Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, Joseph W. O’Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, Igor Vorobyov, Alexander D. MacKerell, Jr., and Richard W. Pastor. The Journal of Physical Chemistry B 2010 114 (23), 7830-7843, DOI: 10.1021/jp101759q</p> <p>[3] CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field. Jumin Lee, Xi Cheng, Jason M. Swails, Min Sun Yeom, Peter K. Eastman, Justin A. Lemkul, Shuai Wei, Joshua Buckner, Jong Cheol Jeong, Yifei Qi, Sunhwan Jo, Vijay S. Pande, David A. Case, Charles L. Brooks, III, Alexander D. MacKerell, Jr., Jeffery B. Klauda, and Wonpil Im. Journal of Chemical Theory and Computation 2016 12 (1), 405-413, DOI: 10.1021/acs.jctc.5b00935</p>
Large DPPC monolayer simulations with Charmm36+OPC @ 310 K (Part 2/2)
<p>DPPC monolayers simulated at a varying area per lipid in the NVT ensemble. The Charmm36 lipid model [1] is employed together with the 4-point OPC water model [2]. Each system contains two monolayers with 256 lipids each. These monolayers are separated by a water slab, and surrounded by vacuum. </p> <p>The number in the filename corresponds to the area per lipid in Ångströms. The starting structures were generated by setting up a POPC monolayer system with an area per lipid of 50 Å^2, followed by a simulation during which the monolayer area was expanded using PLUMED. Next, POPC was replaced by DPPC, and the systems were energy minimized. Systems with area smaller than 51 Å^2 were generated by compressing the DPPC monolayer system with PLUMED.</p> <p>All trajectories, 100–200 ns long (until convergence of surface tension), are simulated with Gromacs 5.0.x [3] using the default Charmm36 monolayer simulations parameters given in the mdp file. This file, together with the topology (.top) and index files (common for all systems) can be obtained from Part 1 of this upload (see below). The topologies (.itp) for the lipids can be obtained from Charmm-GUI and for the OPC water model from https://bioinformatics.cs.vt.edu/~izadi/ .</p> <p>Part 1 of this upload is available at https://doi.org/10.5281/zenodo.345338</p> <p>Matti Javanainen, Antti Lamberg, Lukasz Cwiklik, Ilpo Vattulainen, and O. H. Samuli Ollila. <em>Atomistic Model for Nearly Quantitative Simulations of Langmuir Monolayers</em>, Langmuir <strong>2018</strong> 34 (7), 2565-2572, DOI: 10.1021/acs.langmuir.7b02855</p> <p>[1] DOI: 10.1021/jp101759q<br> [2] DOI: 10.1021/jz501780a<br> [3] DOI: 10.1016/j.softx.2015.06.001</p>
Large DPPC monolayer simulations with Charmm36+OPC @ 298 K (Part 2/2)
<p>DPPC monolayers simulated at a varying area per lipid in the NVT ensemble. The Charmm36 lipid model [1] is employed together with the 4-point OPC water model [2]. Each system contains two monolayers with 256 lipids each. These monolayers are separated by a water slab, and surrounded by vacuum. </p> <p>The number in the filename corresponds to the area per lipid in Ångströms. The starting structures were generated by setting up a POPC monolayer system with an area per lipid of 50 Å^2, followed by a simulation during which the monolayer area was expanded using PLUMED. Next, POPC was replaced by DPPC, and the systems were energy minimized. Systems with area smaller than 51 Å^2 were generated by compressing the DPPC monolayer system with PLUMED.</p> <p>All trajectories, 100–200 ns long (until convergence of surface tension), are simulated with Gromacs 5.0.x [3] using the default Charmm36 monolayer simulations parameters given in the mdp file. This file, together with the topology (.top) and index files (common for all systems) are available in Part 1 of this upload (see below). The topologies (.itp) for the lipids can be obtained from Charmm-GUI and for the OPC water model from https://bioinformatics.cs.vt.edu/~izadi/ .</p> <p>Part 1 of this upload is available at https://doi.org/10.5281/zenodo.345321</p> <p>Matti Javanainen, Antti Lamberg, Lukasz Cwiklik, Ilpo Vattulainen, and O. H. Samuli Ollila. <em>Atomistic Model for Nearly Quantitative Simulations of Langmuir Monolayers</em>, Langmuir <strong>2018</strong> 34 (7), 2565-2572, DOI: 10.1021/acs.langmuir.7b02855</p> <p>[1] DOI: 10.1021/jp101759q<br> [2] DOI: 10.1021/jz501780a<br> [3] DOI: 10.1016/j.softx.2015.06.001</p>
Large POPC monolayer simulations with Charmm36+OPC @ 298 K (Part 2/2)
<p>POPC monolayers simulated at a varying area per lipid in the NVT ensemble. The Charmm36 lipid model [1] is employed together with the 4-point OPC water model [2]. Each system contains two monolayers with 256 lipids each. These monolayers are separated by a water slab, and surrounded by vacuum. </p> <p>The number in the filename corresponds to the area per lipid in Ångströms. The starting structures were generated by setting up a system with an area per lipid of 50 Å^2, followed by a simulation during which the monolayer area was expanded using PLUMED. </p> <p>All trajectories, 100 ns long, are simulated with Gromacs 5.0.x [3] using the default Charmm36 monolayer simulations parameters given in the mdp file. This mdp file, together with the topology (.top) and index files (common for all simulations) can be downloaded from Part 1 of this upload (see below). The topologies (.itp) for the lipids can be obtained from Charmm-GUI and for the OPC water model from https://bioinformatics.cs.vt.edu/~izadi/ .</p> <p>Part 1 of this upload is available at: https://doi.org/10.5281/zenodo.322830</p> <p>The data are discussed in the related publication:</p> <p>Matti Javanainen, Antti Lamberg, Lukasz Cwiklik, Ilpo Vattulainen, and O. H. Samuli Ollila. <em>Atomistic Model for Nearly Quantitative Simulations of Langmuir Monolayers</em>, Langmuir <strong>2018</strong> 34 (7), 2565-2572, DOI: 10.1021/acs.langmuir.7b02855</p> <p>[1] DOI: 10.1021/jp101759q<br> [2] DOI: 10.1021/jz501780a<br> [3] DOI: 10.1016/j.softx.2015.06.001</p> <p> </p>
MD simulation of POPC bilayer with CHARMM36 force field. 7.5 w/l.
<p>MD simulation of POPC (1-palmitoyl-2-oleoyl-phosphatidylcholine) bilayer with CHARMM36 force field. 7.5 w/l.</p> <p>Dataset contains simulation files including trajectories (.xtc) (original production.xtc, and equilibrated and centered ).</p> <p>System: POPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 1500</p> <p>Simulation time: 500 ns</p> <p>Sampling rate: every 10 ps</p> <p>Simulation engine: GROMACS 2022.4</p> <p>Temperature: 300 K</p>
MD simulation of POPC bilayer with CHARMM36 force field. 12 w/l.
<p>MD simulation of POPC (1-palmitoyl-2-oleoyl-phosphatidylcholine) bilayer with CHARMM36 force field. 12 w/l.</p> <p>Dataset contains simulation files including trajectories (.xtc) (original production.xtc, and equilibrated and centered ).</p> <p>System: POPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 2400</p> <p>Simulation time: 500 ns</p> <p>Sampling rate: every 10 ps</p> <p>Simulation engine: GROMACS 2022.4</p> <p>Temperature: 300 K</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>
POPC bilayer, 154 mM NaCl ions, prosECCo75 version of CHARMM36 FF, 310K, gromacs 2021.2
<p>Atomistic molecular dynamic simulation of POPC lipid bilayer in 154 mM NaCl water solution.</p> <p>Water model: TIP3P - CHARMM36 version<br> Lipids: prosECCo75 version of CHARMM36<br> Ions: Sodium: Na_s: DOI: 10.1021/acs.jpcb.5b05221 ; Jungwirth2015 ; scaled<br> Chloride: Cl_2s: DOI: 10.1080/00268976.2013.875231 ; Jungwirth2014b ; scaled</p> <p>README.yaml contains info on simulations files, plus basic analysis (headgroup order parameters, area per lipid)</p>
MD simulation of POPC bilayer with CHARMM36 force field. 5 w/l.
<p>MD simulation of POPC (1-palmitoyl-2-oleoyl-phosphatidylcholine) 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-350-1000ns.xtc).</p> <p>System: POPC 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>Sampling rate: 10 ps</p> <p>Simulation engine: GROMACS 2019.5</p> <p>Temperature: 300 K</p>
MD simulation of POPC bilayer with CHARMM36 force field. 10 w/l.
<p>MD simulation of POPC (1-palmitoyl-2-oleoyl-phosphatidylcholine) 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-75-500ns.xtc).</p> <p>System: POPC 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>Sampling rate: every 10 ps</p> <p>Simulation engine: GROMACS 2019.5</p> <p>Temperature: 300 K</p>
MD simulation of POPC bilayer with CHARMM36 force field. Full hydration 44 w/l.
<p>MD simulation of POPC (1-palmitoyl-2-oleoyl-phosphatidylcholine) bilayer with CHARMM36 force field. Full hydration 44 w/l.</p> <p>Dataset contains simulation files including trajectories (.xtc) (original production.xtc and equilibrated and centered centered-40-500ns.xtc).</p> <p>System: POPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 8880</p> <p>Simulation time: 500 ns</p> <p>Sampling rate: every 10 ps</p> <p>Simulation engine: GROMACS 2019.5</p> <p>Temperature: 300 K</p>
MD simulation of POPC bilayer with CHARMM36 force field. 20 w/l.
<p>MD simulation of POPC (1-palmitoyl-2-oleoyl-phosphatidylcholine) 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-100-500ns.xtc).</p> <p>System: POPC 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>Sampling rate: every 10 ps</p> <p>Simulation engine: GROMACS 2019.5</p> <p>Temperature: 300 K</p>
MD simulation of POPC bilayer with CHARMM36 force field, 100 mM CaCl2
<p>MD simulation of POPC bilayer with CHARMM36 force field, 100 mM CaCl<sub>2</sub></p> <p>Dataset contains simulation files including centered trajectory files. For the ease of the upload, trajectory files (.xtc) are divided to 100ns pieces (Cacl100mM_x-x.xtc)</p> <p>System: POPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 8880</p> <p>Salt: CaCl<sub>2</sub></p> <p>Concentration: 100 mM</p> <p>Number of cations: 16</p> <p>Simulation time: 1000 ns</p> <p>Simulation engine: GROMACS 2019.5</p> <p>Temperature: 300 K</p>
MD simulation of POPC bilayer with CHARMM36 force field, 50 mM CaCl2
<p>MD simulation of POPC bilayer with CHARMM36 force field, 50 mM CaCl<sub>2</sub></p> <p>Dataset contains simulation files including centered trajectory files. For the ease of the upload, trajectory files (.xtc) are divided to 100ns pieces (Cacl_x-xns.xtc)</p> <p>System: POPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 8880</p> <p>Salt: CaCl<sub>2</sub></p> <p>Concentration: 50 mM</p> <p>Number of cations: 8</p> <p>Simulation time: 1000 ns</p> <p>Simulation engine: GROMACS 2019.5</p> <p>Temperature: 300 K</p>
MD simulation of POPC bilayer with CHARMM36 force field, 200 mM CaCl2
<p>MD simulation of POPC bilayer with CHARMM36 force field, 200 mM CaCl<sub>2</sub></p> <p>Dataset contains simulation files including centered trajectory files. For the ease of the upload, trajectory files (.xtc) are divided to 100ns pieces (Cacl200mM_x-x.xtc)</p> <p>System: POPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 8880</p> <p>Salt: CaCl<sub>2</sub></p> <p>Concentration: 200 mM</p> <p>Number of cations: 32</p> <p>Simulation time: 1000 ns</p> <p>Simulation engine: GROMACS 2019.5</p> <p>Temperature: 300 K</p>
MD simulation of POPC bilayer with CHARMM36 force field, 1000 mM CaCl2
<p>MD simulation of POPC bilayer with CHARMM36 force field, 1000 mM CaCl<sub>2</sub></p> <p>Dataset contains simulation files including centered trajectory files. For the ease of the upload, trajectory files (.xtc) are divided to 100ns pieces (Cacl1000mM_x-x.xtc)</p> <p>System: POPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 8726</p> <p>Salt: CaCl<sub>2</sub></p> <p>Concentration: 1000 mM</p> <p>Number of cations: 158</p> <p>Simulation time: 1000 ns</p> <p>Simulation engine: GROMACS 2019.5</p> <p>Temperature: 300 K</p>
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