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Dataset results
119 results for “gromacs”
Simulation data for ECC-CHARMM36 POPC bilayer, 100 lipids/leaflet, 940 mM NaCl, 310K, GROMACS 5.1.4
<p>Simulations of a POPC bilayer with 940 mM of NaC. </p> <p>The sixth from the set of 6 simulations.</p> <p>The goal was to study the effect of scaling the CHARMM FF on the ion binding.</p> <p>Done for the NMRlipids project, see <br> http://nmrlipids.blogspot.fi for more information.</p> <p>A POPC bilayer consisting of 200 lipids (100 per leaflet) <br> is simulated in the presence of 945 mM NaCl. The scaled ECC-Charmm36 <br> model is employed for lipids, the Charmm compatible variant <br> of the tip3p model for water, and the ECC-ions<br> for NaCl. The new extra nonbonded parameters (NB-Fix) were removed.</p> <p> </p> <p>The Charmm36 force field parameters were obtained from http://charmm-gui.org/</p> <p>Charges of head group of POPC were scaled by 0.8, sigmas were scaled by 0.89.</p> <p>In the CHARMM FF, thera are extra sigma and epsilon parameters for 1,4 interactions (these are not present in the lipid14 FF). These parameters were not scaled here.</p> <p>This is the same scaling as used for ECC-POPC</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>The files are in GROMACS format. Trajectory (.xtc) is <br> 610 ns long with data saved every 100 ps.</p> <p>the initial structure (.gro), topology (.top), index file (.ndx), <br> simulation paremeter file (.mdp), binary run input file <br> for GROMACS v. 5.1–> (.tpr) and the energy output file <br> (.edr) are provided. </p>
Simulation data for ECC-CHARMM36 POPC bilayer, 100 lipids/leaflet, 450 mM CaCl2, 310K, GROMACS 5.1.4
<p>Simulations of a POPC bilayer with 450 mM of CaCl_2. </p> <p>The fourth from the set of 6 simulations.</p> <p>The goal was to study the effect of scaling the CHARMM FF on the ion binding.</p> <p>Done for the NMRlipids project, see <br> http://nmrlipids.blogspot.fi for more information.</p> <p>A POPC bilayer consisting of 200 lipids (100 per leaflet) <br> is simulated in the presence of 450 mM CaCl_2. The scaled ECC-Charmm36 <br> model is employed for lipids, the Charmm compatible variant <br> of the tip3p model for water, and the ECC-ions<br> for CaCl_2. The new extra nonbonded parameters (NB-Fix) were removed.</p> <p> </p> <p>The Charmm36 force field parameters were obtained from http://charmm-gui.org/</p> <p>Charges of head group of POPC were scaled by 0.8, sigmas were scaled by 0.89.</p> <p>In the CHARMM FF, thera are extra sigma and epsilon parameters for 1,4 interactions (these are not present in the lipid14 FF). These parameters were not scaled here.</p> <p>This is the same scaling as used for ECC-POPC</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>The files are in GROMACS format. Trajectory (.xtc) is <br> 610 ns long with data saved every 100 ps.</p> <p>the initial structure (.gro), topology (.top), index file (.ndx), <br> simulation paremeter file (.mdp), binary run input file <br> for GROMACS v. 5.1–> (.tpr) and the energy output file <br> (.edr) are provided. </p>
Lysozyme structure (1AKI) for Galaxy GROMACS tutorial
<p>Lysozyme structure (1AKI) for Galaxy GROMACS tutorial</p>
POPS+83%popc lipid bilayer simulation at T298K ran CHARMM_GUI force field and Gromacs
<p>POPS+83%popc lipid bilayer simulation at T298K ran CHARMM_GUI force field and Gromacs. 100ns long trajectory.</p>
Pure POPC bilayer MD simulations with CHARMM36 force field with GROMACS_v2019
<p>500 ns MD simulation of POPC bilayer with CHARMM36 force field at 300 K generated with GROMACS 2019 simulation engine. The system contains 100 POPC lipids per leaflet (200 in total) and 2000 TIP3P water molecules. No, NaCl in the system. This data set contains 500 ns data with 50000 frames (saving frequency is every 10 ps). </p>
MD simulation trajectory of Ternary mixture of POPC/PSM/Chol (2:2:1) at 295 K: Slipids, GROMACS 5.1.4.
<p>MD simulation trajectory files for Ternary mixture of POPC/PSM/Chol [408 POPC, 408 PSM, 208 Chol and 35840 SOL]. The Slipids (2013 version) force field was used with Gromacs 5.1.4. Conditions: T=295K. Data saved every 20 ps. 100 ns trajectory.</p>
Introduction to HPC: molecular dynamics simulations with GROMACS: input files
<p>Introduction to HPC: molecular dynamics simulations with GROMACS: input files</p>
Input files and scripts for Hamiltonian replica-exchange molecular dynamics simulations of intrinsically disordered proteins using a software GROMACS patched with PLUMED
<p>Here we share the necessary files and scripts to run Hamiltonian replica-exchange molecular dynamics simulations of intrinsically disordered protein studied in the preprint uploaded to bioRxiv (doi: https://doi.org/10.1101/2020.06.16.155374). It requires software GROMACS patched with PLUMED.</p>
MD simulation trajectory and related files for POPC bilayer (GAFFlipid, Gromacs 4.5)
<p>Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, GAFFlipid force field (http://dx.doi.org/10.1039/C2SM26007G), 30ns, T=303K, 126 POPC molecules, 3948 water molecules. This data is ran for the nmrlipids.blospot.fi project. More details from nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi. If data is used, please cite nmrlipids.blogspot.fi project and the original publication of the parameters: Dickson et al. Soft Matter, 2012,8, 9617-9627 http://dx.doi.org/10.1039/C2SM26007G.</p>
MD simulation trajectory and related files for POPC bilayer (Chiu et al. Gromos version, Gromacs 4.5)
<p>Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, Chiu et al. force field (http://dx.doi.org/10.1021/jp807056c), 50ns, T=298K, 128 POPC molecules, 3552 water molecules. This data is ran for the nmrlipids.blospot.fi project. More details from nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi. If data is used, please cite nmrlipids.blogspot.fi project and the original publication of the parameters (http://dx.doi.org/10.1021/jp807056c).</p>
Preliminary Gromacs files
<p>Some few simulatitons files for SARS CoV 2</p> <p> </p>
Supplementary information for "GROMACS on AMD GPU-Based HPC Platforms: Using SYCL for Performance and Portability"
<p>GROMACS inputs for the performance benchmarks in the manuscript.</p>
Amyloid-beta 16-22 peptide monomer simulation (150 mM NaCl) with the CHARMM36m force field and Gromacs (Run 2)
<p>MD simulations of the Amyloid-beta 16-22 monomer at 150 mM NaCl concentration with CHARMM36m force field and Gromacs. This repository contains the first out of three independent runs. </p> <p>Files belong to the publication "<a href="https://doi.org/10.1021/acs.jcim.0c01063">https://doi.org/10.1021/acs.jcim.0c01063</a>"</p> <p>All the simulation parameters and force field files are uploaded into this repository. Simulations are done with Gromacs 2018.3</p> <p>Total simulation time is 500 ns. Frames are saved with 100 ps frequency. </p>
Amyloid-beta 16-22 peptide monomer simulation (150 mM NaCl) with the CHARMM36m force field and Gromacs (Run 1)
<p>MD simulations of the Amyloid-beta 16-22 monomer at 150 mM NaCl concentration with CHARMM36m force field and Gromacs. This repository contains the first out of three independent runs. </p> <p>Files belong to the publication "<a href="https://doi.org/10.1021/acs.jcim.0c01063">https://doi.org/10.1021/acs.jcim.0c01063</a>"</p> <p>All the simulation parameters and force field files are uploaded into this repository. Simulations are done with Gromacs 2018.3</p> <p>Total simulation time is 500 ns. Frames are saved with 100 ps frequency. </p>
Immersion enthalpies of nanomaterials (metals, metal oxides, organic chemistry structures) in water and octanol through molecular dynamics simulations with GROMACS and LAMMPS software
<p>Molecular dynamics simulations (free energy calculations) of water interface properties of spherical and Wulff structures nanoparticles (metals, metal oxides and carbon structures) with GROMACS and LAMMPS software.</p>
MD simulation trajectory for POPC bilayer with 128 lipid molecules (CHARMM36, Gromacs 5.1)
<p>Equilibrated POPC lipid bilayer ran with Gromacs 5.1.2 with CHARMM36 lipid forcefield.<br> The simulation is composed of 128 POPC at full hydratation and ran for 500ns at 303K, data saved every 10ps.<br> This data is used in the project "Matching lipid force fields with NMR data". More information at : http://nmrlipids.blogspot.fi/</p>
MD simulation of POPC lipids bilayer at 310K (Berger, Gromacs 3.1.4)
<p>Simulation data and files for POPC Berger simulation at 310K used in publication J. Phys. Chem. B 2007, 111, 3139-3150.</p>
GROMACS Step by Step
<p>This is a GROMACS tutorial.</p>
Gromacs Trajectories of a 200ns simulation of Haloferax volcanii ADH2 in ionic liquids
<p>Gromacs Trajectories of a 200ns simulation of Haloferax volcanii ADH2 in ionic liquids converted from amber trajectories</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
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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.