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Dataset results
299 results for “MD simulation”
MD simulation trajectory of a lipid bilayer: 50/50 mol% POPC/Cholesterol . SLIPIDS, Gromacs 4.6.3. 2016.
<p>MD simulation trajectory files, for fully hydrated POPC + CHOLESTEROL bilayer (50/50 mol%) [256 POPC, 256 CHOL, 20334 WAT]. The SLIPIDS force field was used with Gromacs 4.6.3. Conditions: T=298K. 170 ns each trajectory, last 100 ns analyzed.</p>
POPC/Cholesterol (50:50) lipid membrane, 303K, Charmm36 force field from charmm-gui, simulation files and 200 ns trajectory for Gromacs MD simulation engine v5.1.2
<p>The starting structure was obtained from CHARMM-GUI Membrane Builder v1.7 (http://www.charmm-gui.org/) online tool. [1]</p> <p>All runs were performed with Gromacs 5.1.2 software package and CHARMM36 additive force field parameters obtained from CHARMM-GUI input files [1]. Conditions: T=303, 80 POPC and 80 Cholesterol molecules, 7200 tip3p waters, 200ns trajectory (preceded with equilibration)</p> <p>These data were originally obtained for the nmrlipids.blospot.fi project.</p> <p>Find more details at nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi</p> <p>[1] CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field, J. Lee et al.<strong>,</strong> JCTC,<strong> </strong>DOI: 10.1021/acs.jctc.5b00935</p>
POPC/Cholesterol (70:30) lipid membrane, 303K, Charmm36 force field, simulation files and 200 ns trajectory for Gromacs MD simulation engine v5.1.2
<p>The starting structure was obtained from CHARMM-GUI Membrane Builder v1.7 (http://www.charmm-gui.org/) online tool. [1]</p> <p>All runs were performed with Gromacs 5.1.2 software package and CHARMM36 additive force field parameters obtained from CHARMM-GUI input files [1]. Conditions: T=303, 128 POPC molecules, 5120 tip3p waters, 200ns trajectory (preceded with equilibration)</p> <p>These data were originally obtained for the nmrlipids.blospot.fi project.</p> <p>Find more details at nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi</p> <p>[1] CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field, J. Lee et al.<strong>,</strong> JCTC,<strong> </strong>DOI: 10.1021/acs.jctc.5b00935</p>
MD simulation trajectory of a lipid bilayer: Pure POPC in water. SLIPIDS, Gromacs 4.6.3. 2016.
<p>MD simulation trajectory files, for fully hydrated POPC bilayer [512 POPC, 23943 WAT]. The SLIPIDS force field was used with Gromacs 4.6.3. Conditions: T=298K. 170 ns each trajectory, last 100 ns analyzed.</p>
MD simulation trajectory of a fully hydrated DPPG bilayer @298K: SLIPIDS, Gromacs 5.0.4. 2017.
<p>MD simulation trajectory files, for fully hydrated DPPG bilayer [288 DPPG, 11232 WAT and 288 NA ions]. The SLIPIDS force field was used with Gromacs 5.0.4. Conditions: T=298K. 400 ns trajectory, last 100 ns uploaded for analysis.</p>
MD simulation trajectory of a fully hydrated POPG bilayer: SLIPIDS, Gromacs 5.0.4. 2017.
<p>MD simulation trajectory files, for fully hydrated POPG bilayer [288 POPG, 10664 WAT and 288 NA ions]. The SLIPIDS force field was used with Gromacs 5.0.4. Conditions: T=298K. 250 ns trajectory, last 100 ns uploaded for analysis.</p>
MD simulation trajectory of a fully hydrated DPPE bilayer: SLIPIDS, Gromacs 5.0.4. 2017.
<p>MD simulation trajectory files, for fully hydrated DPPE bilayer [288 DPPE, 9386 WAT]. The SLIPIDS force field was used with Gromacs 5.0.4. Conditions: T=336K. 200 ns trajectory, last 100 ns uploaded for analysis.</p>
MD simulation trajectory of a fully hydrated DPPG bilayer @314K: SLIPIDS, Gromacs 5.0.4. 2017.
<p>MD simulation trajectory files, for fully hydrated DPPG bilayer [288 DPPG, 11232 WAT and 288 NA ions]. The SLIPIDS force field was used with Gromacs 5.0.4. Conditions: T=314K. 200 ns trajectory, last 100 ns uploaded for analysis.</p>
MD simulation trajectory of a fully hydrated DOPS bilayer: SLIPIDS, Gromacs 5.0.4. 2017.
<p>MD simulation trajectory files, for fully hydrated DOPS bilayer [288 DOPS, 11232 WAT and 288 NA ions]. The SLIPIDS force field was used with Gromacs 5.0.4. Conditions: T=303K. 200 ns trajectory, last 100 ns uploaded for analysis.</p>
MD simulation trajectory of a POPC/POPS (4:1) bilayer with 1M CsCl, Berger force field for lipids, Dang's for Cs+ and ffgmx for Cl-
<p>MD simulation trajectory of a POPC/POPS (4:1) bilayer with 1M CsCl (102 POPC, 26 POPS, 4290 WAT, 106 Cs+, 80 Cl-). Additional Cs+ cations added to neutralize the negative charge of POPS. Berger force field for lipids, Dang's for Cs+ (), ffgmx for Cl- are employed. Gromacs 4.0.7, T=310K, 200 ns trajectories were calculated with the last 50 ns stored here).<br> K+ nonbonding parameters (from Dang's Cs+ from JPC B 1999, 103, 8195):<br> sig=0.383086, eps=0.41840</p> <p>Used in:</p> <p>P. Jurkiewicz, L. Cwiklik, A. Vojtiskova, P. Jungwirth, M. Hof, Structure, Dynamics, and Hydration of POPC/POPS Bilayers Suspended in NaCl, KCl, and CsCl <br> <em>BBA Biomembranes </em>2012<em>, 1818, 609-616.</em><br> DOI: 10.1016/j.bbamem.2011.11.033</p>
MD simulation trajectory of a POPC/POPS (4:1) bilayer with 1M KCl, Berger force field for lipids, Dang's for K+ and ffgmx for Cl-
<p>MD simulation trajectory of a POPC/POPS (4:1) bilayer with 1M KCl (102 POPC, 26 POPS, 4290 WAT, 106 K+, 80 Cl-). Additional K+ cations added to neutralize the negative charge of POPS. Berger force field for lipids, Dang's for K+ (), ffgmx for Cl- are employed. Gromacs 4.0.7, T=310K, 200 ns trajectories were calculated with the last 50 ns stored here).K+ nonbonding parameters (from Dang's JPC B 1999, 103, 8195 based on Vacha et al. Biophys. J 2009, 96, 4493.):<br> sig=0.3048655 eps=0.418400</p> <p>Used in:</p> <p>P. Jurkiewicz, L. Cwiklik, A. Vojtiskova, P. Jungwirth, M. Hof, Structure, Dynamics, and Hydration of POPC/POPS Bilayers Suspended in NaCl, KCl, and CsCl <br> <em>BBA Biomembranes </em>2012<em>, 1818, 609-616.</em><br> DOI: 10.1016/j.bbamem.2011.11.033</p>
MD simulation trajectory of a POPC/POPS (4:1) bilayer with 1M NaCl, Berger force field for lipids and ffgmx for ions
<p>MD simulation trajectory of a POPC/POPS (4:1) bilayer with 1M NaCl (102 POPC, 26 POPS, 4290 WAT, 106 Na+, 80 Cl-). Additional Na+ cations added to neutralize the negative charge of POPS. Berger force field for lipids and ffgmx for ions are employed. Gromacs 4.0.7, T=310K, 200 ns trajectories were calculated with the last 50 ns stored here.</p> <p>Used in:</p> <p>P. Jurkiewicz, L. Cwiklik, A. Vojtiskova, P. Jungwirth, M. Hof, Structure, Dynamics, and Hydration of POPC/POPS Bilayers Suspended in NaCl, KCl, and CsCl <br> <em>BBA Biomembranes </em>2012<em>, 1818, 609-616.</em><br> DOI: 10.1016/j.bbamem.2011.11.033</p> <p> </p>
AE1 MD simulation data
<p>MD simulation setups and results for the AE1 system, including the configuration files and corresponding input files (pdb/psf/...) for the equlibration systems (IF1/OF and IF2/IF2), SMD simulations, SMwST simulations and BEUS simulations .</p> <p>Trajectories for the two equilibrium simulations and biased conformational change are also included. Water is removed from the trajectories. </p> <p>Source data for the figures.</p>
Files for MD simulation of the interaction between LCC-ICCG cutinase and PET polymer
<p>500 ns MD simulation of Cutinase adsorption onto the PET surface and cutinase in water.</p> <p>MD simulations were done using Gromacs package</p> <p>Force field:Charmm36</p>
MD simulations from "#GotGlycans: Role of N343 Glycosylation on the SARS-CoV-2 S RBD Structure and Co-Receptor Binding Across Variants of Concern
<p>This folder contains all the MD simulations (saved in frames of 1 ns in PDB format) analysed and discussed in the paper titled "#GotGlycans: Role of N343 Glycosylation on the SARS-CoV-2 S RBD Structure and Co-Receptor Binding Across Variants of Concern" DOI https://doi.org/10.1101/2023.12.05.570076. The naming reflects the specific variant and the presence ('g' or 'gly') or absence ('ng' or 'nogly') of glycosylation at N343 and N331 sites in the SARS-CoV-2 S RBD. Gaussian accelerated MD simulations are indicated with 'gamd', all others represent conventional (deteriministic) sampling. For all details please refer to the original manuscript.</p>
The ReaxFF MD simulation code for the "Mechanistic Investigation of Thermal Plasma Gasification of Polytetrafluoroethylene via Multiscale Simulation Coupled with Experimental Confirmation""
<p>This repository contains the implementation for ReaxFF MD simulation method described in the paper "Mechanistic Investigation of Thermal Plasma Gasification of Polytetrafluoroethylene via Multiscale Simulation Coupled with Experimental Confirmation".</p>
Discovery of Natural Dual Inhibitors from ZINC Database Targeting Thymic Stromal Lymphopoietin (TSLP) and Interleukin-33 (IL-33) as Potential Anti-Allergy Agents - MD Simulation XVG Files and Complex PDB Files (Docking Results)
<p>This repository contains input and output files of MD simulations along with MM/PBSA related files</p> <p>Manuscript Title: Discovery of Natural Dual Inhibitors from ZINC Database Targeting Thymic Stromal Lymphopoietin (TSLP) and Interleukin-33 (IL-33) as Potential Anti-Allergy Agents</p> <p> </p>
Design and assembly of core/shell nanostructures as investigated by microfluidics and molecular dynamics simulation_dataset_DLS_TEM_MD
<p><span>He we like to publish data related to modified and non-modified MSN cores analysed using microfluidics platform against acetalated dextran (AcDEX)/spermine modified acetalated dextran (SpAcDEX) polymers. </span></p> <p><span>The data contains Dynamic light scattering (DLS) and TEM images which help us to to the demarcation of combinations which formed successful core/shell particles along with, <em>in-silico</em> modelling and molecular dynamics (MD) simulations data showing molecular interactions between the core particles and <a>the encapsulant </a></span><span><span></span></span><span>polymer. </span></p>
Exploring Kv1.2 channel inactivation through MD simulations and network analysis
<p>MD equilibration trajectories of Kv1.2 WT and mutants in dcd format can be visualized using visualization tools such as VMD or PyMol after uploading the topology file (.prmtop).</p>
MD simulation trajectory of DOG/POPE bilayer and related files
<p>Raw simulation trajectory data of pre-equiblirated DOG/POPE bilayer and related files from all-atom molecular dynamics simulations. Simulations have been performed with GROMACS-2018.6 with Lipid17 forcefield and TIP3P water model. The trajectory is 0-2100 ns, and we have disregarded the first 100 ns in our analysis.</p> <p>The system in the trajectory consists of 12 DOG, 116 POPE and 6400 water molecules. Temperature 310 K, pressure 1 bar.</p>
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.