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56 results for “DPPC”
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>
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>
Simulations of a DPPC bilayer at different temperatures
<p>Simulations aimed to estimate the melting point of pure DPPC membranes in the Slipids force field. Simulations performed at 300, 305, and 310 K. The simulations were 500 ns (300 K & 305 K) or 300 ns (310 K) long. Full details of simulations available in the related manuscript, where they are also carefully analyzed:</p> <p>Nanoscale Membrane Domain Formation Driven by Cholesterol</p> <p>by Matti Javanainen, Hector Martinez-Seara, and Ilpo Vattulainen</p> <p>Scientific Reports 7: 1143 (2017)</p>
212 DPPC Molecules bilayer in pure Water, simulated at temperatures ranging from 288K to 358K
<p><strong>Publication:</strong> A machine learning study of the two states model for lipid bilayer phase transitions</p> <p><strong>Published on:</strong> 12 August 2020</p> <p><strong>Journal</strong>: <a href="https://pubs.rsc.org/en/content/articlelanding/2020/cp/d0cp02058c?fbclid=IwAR1Nzre773-uWrlf4vpc7dzEGoQYeWxSKPESSE9BNA3VGeg6xvBdkFOvEo0#!divAbstract"><em>Phys. Chem. Chem. Phys.</em></a>, 2020, DOI: 10.1039/D0CP02058C</p> <p><strong>Description</strong>: Simulation files used to train our machine learning algorithm to identify the thermodynamic phase of individual lipid molecules in a bilayer, as well as the simulation files analysed by the machine learning models. Code source for the ML algorithm can be found on <a href="https://github.com/vivien-walter/mllpa">Github</a>.</p> <p>The training files are named gel.gro and fluid.gro. They respectively correspond to the final frame of the systems simulated at 288K and 358K.</p> <p>All other files are the files analysed by the machine learning models.</p> <p><strong>System composition:</strong></p> <ul> <li>DPPC molecules: 212 with 130 atoms each</li> <li>Water molecules: 29,826 with 3 atoms each </li> <li>Simulation box dimensions (approx.): 8 x 8 x 20 nm</li> </ul> <p><strong>Simulation details:</strong></p> <ul> <li>Software: Gromacs (v. 2016.4)</li> <li>Forcefield: Charmm36 (v. June 2015) - Water: TIP3P</li> <li>Thermostat: Nose-hoover (0.4ps, 2 groups)</li> <li>Barostat: Parrinello-Rahman semi-isotropic (2.0ps, 1.0 bar on each axis, 4.5e-5 bar-1)</li> <li>Duration: 50 ns</li> </ul>
Simulations of DPPC monolayers with CaCl_2
<p>Description to follow.</p> <p>Itp files to be linked.</p>
Simulations of DPPC monolayers with NaCl
<p>Description to follow.</p> <p>Itp files to be linked.</p> <p> </p>
Simulations of DPPC monolayers with MgCl_2
<p>Description to follow.</p> <p>Itp files to be linked.</p>
Simulations of DPPC monolayers without ions
<p>Description to follow.</p> <p>Itp files to be linked.</p>
DPPC+CHOL@322K,1µs
<p>CHARMM36 MD simulation of 224 DPPC + 32 CHOL @322K; 1µs; 20 000 frames.</p> <p>This was preceded by 100ns equilibration.</p>
DPPC+CHOL@320K,1µs
<p>CHARMM36 MD simulation of 224 DPPC + 32 CHOL @320K; 1µs; 20 000 frames.</p> <p>This was preceded by 100ns equilibration.</p>
DPPC+CHOL@317K,1µs
<p>CHARMM36 MD simulation of 224 DPPC + 32 CHOL @317K; 1µs; 20 000 frames.</p> <p>This was preceded by 100ns equilibration.</p>
DPPC+CHOL@325K,1µs
<p>CHARMM36 MD simulation of 224 DPPC + 32 CHOL @325K; 1µs; 20 000 frames.</p> <p>This was preceded by 100ns equilibration.</p>
DPPC+CHOL@327K,1µs
<p>CHARMM36 MD simulation of 224 DPPC + 32 CHOL @327K; 1µs; 20 000 frames.</p> <p>This was preceded by 100ns equilibration.</p>
OMPG protein in DPPC membrane with various solvent viscosities - part2
<p>This set of data is used to fit the translational Saffman-Delbruck model to systems of different fluid viscosity.<br> Each system contains:</p> <ul> <li>1 OMPG</li> <li>800 DPPC</li> <li>8000 W</li> <li>800 WF (anitfreeze)</li> <li>111 NA+</li> <li>95 CL-</li> </ul> <p>At each viscosity, 5 replicas are performed to decrease the uncertainty.</p>
OMPG protein in DPPC membrane with various solvent viscosities - part1
<p>This set of data is used to fit the translational Saffman-Delbruck model to systems of different fluid viscosity.<br> Each system contains:</p> <ul> <li>1 OMPG</li> <li>800 DPPC</li> <li>8000 W</li> <li>800 WF (anitfreeze)</li> <li>111 NA+</li> <li>95 CL-</li> </ul> <p>At each viscosity, 5 replicas are performed to decrease the uncertainty.</p> <p> </p>
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