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220 results for “force fields”
Systematic evaluation of ReaxFF reactive force fields for biochemical applications
<p>The tar archive contains supporting information to accompany the publication. The data includes the ReaxFF force field files, XYZ and BGF geometry files for amino acid conformers and dipeptides, pathways of initial DNEB interpolations and full connected pathways of condensation reactions.</p>
Phoshorene Solvated in [EMIM][BF4]. Force field files and MD systems
<p>Phoshorene Solvated in [EMIM][BF4]. Force field files and MD systems</p>
DESO-water force fields and MD systems
<p>DESO-water force fields and MD systems</p>
Dataset for manuscript: Boosting ensemble refinement with transferable force field corrections: synergistic optimization for molecular simulations
<p>See https://github.com/bussilab/force-field-ensemble-refinement for analysis scripts</p>
Input files for T4 lysozyme free energy calculations with DMBIS non-bonded force field parameters
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MD simulation of POPC bilayer with OPLS4 force field. 12 w/l.
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"Methodological and force field effects in the molecular dynamics-based prediction of binding free energies of host-guest systems"
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MD simulation of DMPC bilayer with OPLS4 force field. 5 w/l.
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MD simulation of DMPC bilayer with OPLS4 force field. 10 w/l.
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MD simulation of DMPC bilayer with OPLS4 force field. 20 w/l.
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MD simulation of DMPC bilayer with OPLS4 force field. Full hydration.
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Output from the Glacier Energy and Mass Balance (GEMB v1.0) forced with 3-hourly RACMO fields, Greenland and Antarctica 1979-2014
<p>These model output are those presented in the manuscript that provides the first description of version 1.0 of the open-source Glacier Energy and Mass Balance model. GEMB is a column model of ice sheet and glacier surface-atmospheric energy and mass exchange as well as firn state. GEMB has been integrated into the open-source Ice-Sheet and Sea-level System Model which can be downloaded at https://issm.jpl.nasa.gov/. Here, GEMB is forced with 3-hourly RACMO output from 1979-2014. </p>
Benzalkonium chlorides MARTINI force field parameters
<p>Benzalkonium chlorides MARTINI force field parameters (BAK8, BAK12, CKC).</p>
Research and Evaluation of Allosteric Protein Specific Force Field Based on Deep Learning
<p>All trajectories for evaluating APSF force field</p>
Pure POPC Membrane with 650mM NaCl simulations using Drude Polarizable Force Field and OpenMM
<p>500 ns MD simulation of pure POPC membrane using Charmm-Drude polarizable force field. The system contains 128 POPC lipids, 77 NaCl, and 6400 SWM4 water molecules.</p> <p>The simulation have been performed using OpenMM 7.4.1</p> <p>Before running the Drude simulation, the system has been equilibriated using Charmm36 force field for 200 ns. The last frame of that simulation was used to generate Drude polarizable model. The first 100 ns of the Drude simulation has been discarded from this dataset.</p> <p>wrapped.dcd has a frame saving frequency of 100 ps.</p> <p><strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the wrapped_full.dcd trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "wrapped_full_fixed_dt.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps. </strong></p> <p><strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong></p> <p><strong>This simulation consists of 5 sub-trajectories, each of which starts from the last frame of the previous one and runs for 100 ns. These trajectories (originally in dcd format) were concatenated and saved in xtc format with MDAnalysis.</strong></p>
Pure POPC Membrane with 350mM NaCl simulations using Drude Polarizable Force Field and OpenMM
<p>500 ns MD simulation of pure POPC membrane using Charmm-Drude polarizable force field. The system contains 128 POPC lipids, 41 NaCl, and 6400 SWM4 water molecules.</p> <p>The simulation have been performed using OpenMM 7.4.1</p> <p>Before running the Drude simulation, the system has been equilibriated using Charmm36 force field for 200 ns. The last frame of that simulation was used to generate Drude polarizable model. The first 100 ns of the Drude simulation has been discarded from this dataset.</p> <p>wrapped.dcd has a frame saving frequency of 100 ps.</p> <p><strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the wrapped_full.dcd trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "wrapped_full_fixed_dt.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps. </strong></p> <p><strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong></p> <p><strong>This simulation consists of 5 sub-trajectories, each of which starts from the last frame of the previous one and runs for 100 ns. These trajectories (originally in dcd format) were concatenated and saved in xtc format with MDAnalysis.</strong></p>
Pure POPC Membrane with 450mM CaCl2 simulations using Drude Polarizable Force Field and OpenMM
<p>500 ns MD simulation of pure POPC membrane using Charmm-Drude polarizable force field. The system contains 128 POPC lipids, 52 CaCl2, and 6400 SWM4 water molecules. </p> <p>The simulation have been performed using OpenMM 7.4.1 Frames are saved in every 10 ps. Before running the Drude simulation, the system has been equilibriated using Charmm36 force field for 200 ns. The last frame of that simulation was used to generate Drude polarizable model. The first 100 ns of the Drude simulation has been discarded from this dataset.</p> <p>wrapped.dcd has a frame saving frequency of 100 ps.</p> <p><strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the wrapped_full.dcd trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "wrapped_full.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps. </strong></p> <p><strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong></p> <p><strong>This simulation consists of 5 sub-trajectories, each of which starts from the last frame of the previous one and runs for 100 ns. These trajectories (originally in dcd format) were centered with VMD command "pbc wrap -center origin -centersel lipid -compound residue -all", concatenated and saved in xtc format with MDAnalysis.</strong></p> <p> </p>
MD simulations of the Sec61/TRAP/ribosome complex and various subcomplexes with CHARMM36 force field
<p>Simulation data for the Sec61/TRAP/ribosome complex and its subcomplexes (TRAP alone, Sec61 alone, as well as Sec61 with TRAP) embedded in an ER membrane mimic. Simulations are performed using GROMACS and with the all-atom CHARMM family of force fields. The uploaded trajectories (xtc) contain the coordinates stored every 2 ns of the 2-µs-long simulations. The output energy files (edr), run input files (tpr), and the continue points (cpt) at 2 µs are provided. </p> <p>This upload also contains data for the Sec61/TRAP/ribosome complex simulated in a POPC bicelle. This simulation is 1 µs long and the coordinates are stored every 1 ns.</p> <p>All required input files are also provided to regenerate the run input file: initial structures (gro), index files (ndx), topologies (top and itp), and the simulation parameter file (mdp). Details of the setup, simulation, and analysis of the systems is available in the preprint:</p> <p>https://doi.org/10.1101/2022.09.30.510141</p> <p> </p>
Data for the paper "Efficient calculation of self magnetic field, self-force, and self-inductance for electromagnetic coils. II. Rectangular cross-section"
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Simulations of POPC:POPG 1:1 membranes with varying levels of CaCl_2 using the Slipids force field
<p>Simulations of POPC/POPG lipid bilayers consisting of a total of 256 lipids (128 POPC + 128 POPG) spread equally between the two leaflets. The initial CaCl_2 concentration in the water phase was either 0, 100, 200, 500, or 1000 mM. Na+ was used as the counterion for the POPG charges. The simuatlions were performed using the Slipids model, available at http://www.fos.su.se/~sasha/SLipids/ . The Dang ion parameters were used, and they were obtained from https://bitbucket.org/hseara/ions/ . The common simulation parameters are given in the md.mdp file. The simulations are 1500 ns long (except CA0, which is 500 ns long), and the "extend" files contain the last 1000 ns of the outputs. The "extend" continue points should also be used to extend the simulations beyond 1500 ns. All relevant input and output files are provided to repeat or extend the simulations.</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.