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37 results for “POPE”
OPLS-UA POPE Simulations (versions 1 and 2) 303 K with vdW on H atoms
<p>Two OPLS-UA POPE bilayer simulations performed using GROMACS 4.5.7 for 200 ns with different starting velocities. Simulations were performed with a 1.0 nm cut-off with PME for the Coulombic and a 1.0 nm cut-off for the van der Waals interactions interactions. These simulations were performed at 303 K with a 128 lipid bilayer. The full trajectories are provided bar the initial 100 ns. The starting structure was made through the conversion of an equilibrated OPLS-UA POPC membrane. The PE parameters were constructed by modifying the OPLS-UA POPC of Ulmschneider and Ulmschnider with the standard OPLS lysine parameters and the addition of LJ parameters on the hydrogen atoms in the head group (designed to increase the area per lipid).</p>
OPLS-UA POPE Simulations (versions 1 and 2) 303 K
<p>Two OPLS-UA POPE bilayer simulations performed using GROMACS 4.5.7 for 200 ns with different starting velocities. Simulations were performed with a 1.0 nm cut-off with PME for the Coulombic and a 1.0 nm cut-off for the van der Waals interactions interactions. These simulations were performed at 303 K with a 128 lipid bilayer. The full trajectories are provided bar the initial 100 ns. The starting structure was made through the conversion of an equilibrated OPLS-UA POPC membrane. The PE parameters were constructed by modifying the OPLS-UA POPC of Ulmschneider and Ulmschnider with the standard OPLS lysine parameters.</p>
CHARMM36-UA POPE Simulations (versions 1 and 2) 310 K (NOTE: hexagonal membrane and POPE is called PEUA)
<p>Two CHARMM36-UA POPE bilayer simulations performed using GROMACS 5.0.6 for 200 ns with different starting velocities. Simulations were performed with the standard CHARMM36 settings: a 1.2 nm cut-off with PME for the Coulombic interactions and a 1.2 nm cut-off for the van der Waals interactions with the forces switched off at 1.0 nm. These simulations were performed at 310 K with a 336 hexagonal lipid bilayer. The full trajectories are provided bar the initial 100 ns. The starting structure of the membrane was made by reverse mapping an equilibrated MARTINI POPE bilayer (constructed with the INSANE script).</p>
Slipids POPE Simulations (versions 1 and 2) 310 K (NOTE: hexagonal membrane)
<p>Two Slipids POPE bilayer simulations performed using GROMACS 5.0.6 for 200 ns with different starting velocities. Simulations were performed with a 1.0 nm cut-off with PME for the Coulombic and a 1.0 nm cut-off for the van der Waals interactions interactions. These simulations were performed at 310 K with a 336 hexagonal lipid bilayer. The full trajectories are provided bar the initial 100 ns. The starting structure of the membrane was made by reverse mapping an equilibrated MARTINI POPE bilayer (constructed with the INSANE script).</p>
GROMOS 43A1-S3 POPE Simulations (versions 1 and 2) 313 K (NOTE: anisotropic pressure coupling)
<p>Two GROMOS 43A1-S3 POPE bilayer simulations performed using GROMACS 4.0.7 for 200 ns with different starting velocities. Simulations were performed with the standard 43A1-S3 settings: a 1.0 nm cut-off with PME for the Coulombic interactions and a twin-range 1.0/1.6 nm cut-off for the van der Waals interactions. These simulations were performed at 313 K with a 128 lipid bilayer and used anisotropic pressure coupling. The full trajectories are provided bar the initial 100 ns. The starting structure was made through the conversion of an equilibrated GROMOS 43A1-S3 POPC membrane.</p>
Simulation of a POPE bilayer at 310K with the CHARMM36 force field
<p>A bilayer of 144 POPE lipids (72 per leaflet) simulated in water (40 molecules per lipid) for 500 ns using the CHARMM36 force field [1] using GROMACS v. 2018.6 [2]. Topologies are obtained from CHARMM-GUI [3].</p> <p>[1] <strong>DOI: </strong>10.1021/jp101759q</p> <p>[2] <strong>DOI: </strong>10.1016/j.softx.2015.06.001</p> <p>[3] <strong>DOI: </strong>10.1021/acs.jctc.5b00935</p> <p> </p>
MD simulation trajectory of POPE bilayer and related files
<p>Simulation trajectory pre-equiblirated POPE bilayer and related files from all-atom molecular dynamics simulations. Simulations have been performed with GROMACS-2021.2 with Lipid17 forcefield and TIP3P water model. The trajectory is 0-1000 ns, and we have disregarded the first 100 ns in our analysis.</p> <p>The system in the trajectory consists of 128 POPE and 6400 water molecules. Temperature 310 K, pressure 1 bar.</p> <p>Publication: <a href="https://doi.org/10.1016/j.bbamem.2022.183961">https://doi.org/10.1016/j.bbamem.2022.183961</a></p>
OpenMM simulations of POPE 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.7872447</span> have been concatenated into a single 200 ns long trajectory in xtc format by Batuhan Kav using MDAnalysis.</p>
Palace of the Popes, Avignon, France
Palais des Papes, Avignon, Southern France Source: Objaverse 1.0 / Sketchfab
Dataset for: Fast retreat of Pope, Smith, and Kohler glaciers in West Antarctica observed by satellite interferometry
Open the record for dataset details and reuse information.
Pure POPE OpenFF Fix Attempt 1
<p>200 ns 64:64 POPE bilayer hydrated with 5000 TIP3P waters.</p>
Pure--No Build--POPE OpenFF Fix Attempt 1
<p>Reused 200 ns 64:64 POPE bilayer hydrated with 5000 TIP3P waters.</p>
Simulation of POPC:POPE 1:1 membrane, model by Maciejewski and Rog
<p>A POPC:POPE 1:1 bilayer with 64 lipids per leaflet is simulated for 300 ns using the model by Maciejewski and Rog [1,2] and Gromacs simulation engine version 2019.4. The trajectory (.xtc) is saved every 100ps. The simulation parameters (.mdp), the energy file (.edr), the continue point to extend the simulation (.cpt), the run input parameters (.tpr), and the final structure (.gro) are also given. The lipid topologies (.itp) are attached, and they are obtained from the authors. Note that unlike in the original paper [2], buffered Verlet lists are used for efficiency.</p> <p>[1] DOI: 10.1016/j.dib.2016.03.067</p> <p>[2] DOI: 10.1021/jp5016627</p>
Pure POPE membrane simulations with the AMOEBA force field at 310K (OpenMM)
<p>MD simulation data of a pure POPE membrane with the AMOEBA force field generated with the OpenMM simulation engine at 310K.</p> <p>Parameters from https://doi.org/10.1080/00268976.2018.1436201</p>
Popes pilskalns (ortofoto)
Popes pilskalna 3D modelis ar ortofoto pārklājumu. Koordinātas: 57.40652,21.8471 https://www.latvijas-pilskalni.lv/popes-pilskalns/ Source: Objaverse 1.0 / Sketchfab
FIGURE 2 in Anthias albofasciatus Fowler and Bean, 1930, a junior synonym of Tosana niwae Smith and Pope, 1906 (Teleostei: Serranidae: Anthiadinae)
FIGURE 2. Radiographs of holotypes of A) Anthias albofasciatus, USNM 89988, 74.9 mm SL; B) Tosana niwae, USNM 55618, 83.3 mm SL. (Radiographs by S. Raredon)
FIGURE 4. Tosana niwae A in Anthias albofasciatus Fowler and Bean, 1930, a junior synonym of Tosana niwae Smith and Pope, 1906 (Teleostei: Serranidae: Anthiadinae)
FIGURE 4. Tosana niwae A) aquarium photo of ca 25 mm SL juvenile from Okinawa, Ryukyu Islands, Japan (photo by Y.K. Tea); B) KPM-NI 35479 (image KPM-NR 107491B), 106 mm SL, freshly dead male, off Odawara, Honshu, Japan (© Kanagawa Prefectural Museum of Natural History; photo by H. Senou); C) aquarium photo of ca 90 mm SL male from the Izu Peninsula, Honshu, Japan (photo by K. Zeze).
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