Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
220
datasets available to search
ShareScore release 0.9.0
Dataset results
220 results for “force fields”
Underlying data for "Evaluation of solvation free energies for small molecules with the AMOEBA polarizable force field"
<p>This dataset provides the parameters and results generated for the study "Evaluation of solvation free energies for small molecules with the AMOEBA polarizable force field"</p> <p>Contents of dataset:<br /> PARAMETERS.tar.gz<br /> A gzipped and tar'd directory with the parameters of all solutes sorted by solvent for AMOEBA and GAFF force field. This parameters directory is distributed to 4 different subdirectories: a)chloroform (21 solutes) b)toluene (21 solutes) c)dmso (6 solutes) d)acetonitrile (6 solutes). Each solvent includes two set of parameters for each solute (AMOEBA and GAFF).</p> <p>RESULTS.tar.gz<br /> A gzipped and tar'd directory with the solvation free energy results of all solutes in kcal/mol, with AMOEBA and GAFF force fields, for each solvent, in text format. A single set of conditions for a single solute is one row in the text files. The first column represents the experimental data, the remaining columns (2, 3 and 4) correspond to the three repeat simulations.</p>
POPC with 0, 10, 20, and 30 mol-% of cholesterol at 310 K. Charmm36 force field. *OBSOLETE*
<p>A POPC bilayer consisting of 200 lipids (100 per leaflet) <br> is simulated in the presence of 0% (0 molecules), 10 %<br> (22 molecules), 20 % (50 molecules), or 30 % (86 molecules)<br> of cholesterol. The Charmm36 model [1] is employed for lipids and the Charmm-compatible variant of the tip3p model for water.</p> <p>The Charmm36 force field parameters were obtained from CHARMM-GUI [2] at http://www.charmm-gui.org</p> <p> </p> <p>*** IMPORTANT ***</p> <p>These simulations were performed using an erroneous charmm36.itp file provided by version 1.7 of CHARMM-GUI, as stated in http://www.charmm-gui.org/?doc=log : "The multiplicity (of dihedral parameters) issue in GROMACS inputs; this issue affects the systems generated from August 21<sup>th</sup> 2015 to December 9<sup>th</sup> 2015." Due to the bad .itp, the deuterium order parameters of C2, as well as the glycerol group, show strange behavior. The systems simulated with the correct itp file can be accessed at: DOI: 10.5281/zenodo.159759.</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>The files are in GROMACS format. Trajectory (.xtc) is 100 ns long with data saved every 100 ps. Additionally, the initial structure (.gro), topology (.top), index file (.ndx), simulation paremeter file (.mdp), binary run input file for GROMACS v. 5.0–> (.tpr) and the energy output file (.edr) are provided. </p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>[1] Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types</p> <p>Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, Joseph W. O’Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, Igor Vorobyov, Alexander D. MacKerell, Jr., and Richard W. Pastor</p> <p>The Journal of Physical Chemistry B 2010 114 (23), 7830-7843</p> <p>DOI: 10.1021/jp101759q</p> <p> </p> <p>[2] CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field</p> <p>Jumin Lee, Xi Cheng, Jason M. Swails, Min Sun Yeom, Peter K. Eastman, Justin A. Lemkul, Shuai Wei, Joshua Buckner, Jong Cheol Jeong, Yifei Qi, Sunhwan Jo, Vijay S. Pande, David A. Case, Charles L. Brooks, III, Alexander D. MacKerell, Jr., Jeffery B. Klauda, and Wonpil Im</p> <p>Journal of Chemical Theory and Computation 2016 12 (1), 405-413</p> <p>DOI: 10.1021/acs.jctc.5b00935</p>
Simulations of DPPC/Cholesterol bilayers with the Slipids force field, part 2/2
<p>Simulation data related to our publication "Nanoscale Membrane Domain Formation Driven by Cholesterol" (DOI:10.1038/s41598-017-01247-9), part 2/2. Part 1/2 of the data are in the Zenodo record (DOI:10.5281/zenodo.439066). Please note that the description below covers both parts.</p> <p>Data for both cholesterol-free calibration simulations (letters in Table S1 and Fig. 1) and for cholesterol-containing simulations (numbers in Table S1 and Fig. 1) are included. The files are named as "dppc-X-Y.Z", where X is the cholesterol concentration, Y the simulation temperature (not shifted, see the paper), and Z defines the file type (in GROMACS formats): xtc for trajectory, edr for energy file, tpr for the simulation input file, and .cpt for the checkpoint file. The index file (.ndx) and the topology file (.top) are common among systems with equal cholesterol concentration. The simulation parameter file (.mdp) is common for all simulations, only the target temperature of the thermostat needs to be adjusted. Simulation lengths vary between 300 and 1400 ns, and the trajectories are written every 100 ps. Further information on the setup and composition of the simulated systems is available in the paper.</p> <p>The Slipids force field [1,2,3] is employed, and the topologies (.itp) are available at http://www.fos.su.se/~sasha/SLipids/</p> <p>All simulations were performed with Gromacs 4.6.x </p> <p> </p> <p>[1] Derivation and Systematic Validation of a Refined All-Atom Force Field for Phosphatidylcholine Lipids. Joakim P. M. Jämbeck and Alexander P. Lyubartsev, The Journal of Physical Chemistry B 2012 116 (10), 3164-3179, DOI: 10.1021/jp212503e<br> [2] An Extension and Further Validation of an All-Atomistic Force Field for Biological Membranes. Joakim P. M. Jämbeck and Alexander P. Lyubartsev, Journal of Chemical Theory and Computation 2012 8 (8), 2938-2948, DOI: 10.1021/ct300342n<br> [3] Another Piece of the Membrane Puzzle: Extending Slipids Further. Joakim P. M. Jämbeck and Alexander P. Lyubartsev, Journal of Chemical Theory and Computation 2013 9 (1), 774-784, DOI: 10.1021/ct300777p</p>
Simulations of DPPC/Cholesterol bilayers with the Slipids force field, part 1/2
<p>Simulation data related to our publication "Nanoscale Membrane Domain Formation Driven by Cholesterol" (DOI:10.1038/s41598-017-01247-9), part 1/2. Part 2/2 of the data are in the Zenodo record (DOI:10.5281/zenodo.439080). Please note that the description below covers both parts.</p> <p>Data for both cholesterol-free calibration simulations (letters in Table S1 and Fig. 1) and for cholesterol-containing simulations (numbers in Table S1 and Fig. 1) are included. The files are named as "dppc-X-Y.Z", where X is the cholesterol concentration, Y the simulation temperature (not shifted, see the paper), and Z defines the file type (in GROMACS formats): xtc for trajectory, edr for energy file, tpr for the simulation input file, and .cpt for the checkpoint file. The index file (.ndx) and the topology file (.top) are common among systems with equal cholesterol concentration. The simulation parameter file (.mdp) is common for all simulations, only the target temperature of the thermostat needs to be adjusted. Simulation lengths vary between 300 and 1400 ns, and the trajectories are written every 100 ps. Further information on the setup and composition of the simulated systems is available in the paper.</p> <p>The Slipids force field [1,2,3] is employed, and the topologies (.itp) are available at http://www.fos.su.se/~sasha/SLipids/</p> <p>All simulations were performed with Gromacs 4.6.x </p> <p> </p> <p>[1] Derivation and Systematic Validation of a Refined All-Atom Force Field for Phosphatidylcholine Lipids. Joakim P. M. Jämbeck and Alexander P. Lyubartsev, The Journal of Physical Chemistry B 2012 116 (10), 3164-3179, DOI: 10.1021/jp212503e<br> [2] An Extension and Further Validation of an All-Atomistic Force Field for Biological Membranes. Joakim P. M. Jämbeck and Alexander P. Lyubartsev, Journal of Chemical Theory and Computation 2012 8 (8), 2938-2948, DOI: 10.1021/ct300342n<br> [3] Another Piece of the Membrane Puzzle: Extending Slipids Further. Joakim P. M. Jämbeck and Alexander P. Lyubartsev, Journal of Chemical Theory and Computation 2013 9 (1), 774-784, DOI: 10.1021/ct300777p</p>
Simulations of large POPC bilayers using the Charmm36 force field.
<p>An earlier simulation (DOI:10.5281/zenodo.159759) of a POPC bilayer consisting of 200 lipids (100 per leaflet) is extended to 4 and 9 times larger (800 and 1800 lipids) and simulated for 100 ns using Gromacs v5.1.x [1]. The Charmm36 model [2] is employed for lipids and the Charmm-compatible variant of the tip3p model for water.</p> <p>The Charmm36 force field parameters were obtained from CHARMM-GUI [3] at http://www.charmm-gui.org</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>The files are in GROMACS format. The number in the file name corresponds to how many times larger the system is compared to that in (DOI:10.5281/zenodo.159759), either 4 (2x2) or 9 (3x3). Trajectories (.xtc) is 100 ns long with data saved every 100 ps. Additionally, the topology (.top), binary run input file for GROMACS v. 5.0–> (.tpr), the continue point file (.cpt), and the energy output file (.edr) are provided. The provided simulation paremeter file (.mdp) is common for both simulations. </p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>[1] GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. Mark J. Abraham, Teemu Murtola, Roland Schulz, Szilárd Páll, Jeremy C. Smith, Berk Hess, and Erik Lindahl. SoftwareX 2015 1–2, 19–25, DOI: 10.1016/j.softx.2015.06.001</p> <p>[2] Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types. Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, Joseph W. O’Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, Igor Vorobyov, Alexander D. MacKerell, Jr., and Richard W. Pastor. The Journal of Physical Chemistry B 2010 114 (23), 7830-7843, DOI: 10.1021/jp101759q</p> <p>[3] CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field. Jumin Lee, Xi Cheng, Jason M. Swails, Min Sun Yeom, Peter K. Eastman, Justin A. Lemkul, Shuai Wei, Joshua Buckner, Jong Cheol Jeong, Yifei Qi, Sunhwan Jo, Vijay S. Pande, David A. Case, Charles L. Brooks, III, Alexander D. MacKerell, Jr., Jeffery B. Klauda, and Wonpil Im. Journal of Chemical Theory and Computation 2016 12 (1), 405-413, DOI: 10.1021/acs.jctc.5b00935</p>
Screener and Enumerator with Force-Field Optimization (SEFFO): algorithm for searching adsorption sites and configurations on 2D materials
<p>See ref:</p> <p> </p> <p>(submission stage)</p>
MD simulation of POPC bilayer with CHARMM36 force field. 7.5 w/l.
<p>MD simulation of POPC (1-palmitoyl-2-oleoyl-phosphatidylcholine) bilayer with CHARMM36 force field. 7.5 w/l.</p> <p>Dataset contains simulation files including trajectories (.xtc) (original production.xtc, and equilibrated and centered ).</p> <p>System: POPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 1500</p> <p>Simulation time: 500 ns</p> <p>Sampling rate: every 10 ps</p> <p>Simulation engine: GROMACS 2022.4</p> <p>Temperature: 300 K</p>
MD simulation of POPC bilayer with CHARMM36 force field. 12 w/l.
<p>MD simulation of POPC (1-palmitoyl-2-oleoyl-phosphatidylcholine) bilayer with CHARMM36 force field. 12 w/l.</p> <p>Dataset contains simulation files including trajectories (.xtc) (original production.xtc, and equilibrated and centered ).</p> <p>System: POPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 2400</p> <p>Simulation time: 500 ns</p> <p>Sampling rate: every 10 ps</p> <p>Simulation engine: GROMACS 2022.4</p> <p>Temperature: 300 K</p>
MD simulation of DMPC bilayer with CHARMM36 force field. 20 w/l
<p>MD simulation of DMPC bilayer with CHARMM36 force field. 20 w/l.</p> <p>Dataset contains simulation files including trajectories (.xtc) (original production.xtc, and equilibrated and centered centered_pbcmol-20-500ns.xtc).</p> <p>System: DMPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 4000</p> <p>Simulation time: 500 ns</p> <p>Simulation engine: GROMACS 2019.5</p> <p>Temperature: 314 K</p>
MD simulation of DMPC bilayer with CHARMM36 force field. 10 w/l.
<p>MD simulation of DMPC bilayer with CHARMM36 force field. 10 w/l.</p> <p>Dataset contains simulation files including trajectories (.xtc) (original production.xtc, and equilibrated and centered centered_pbcmol-50-500ns.xtc).</p> <p>System: DMPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 2000</p> <p>Simulation time: 500 ns</p> <p>Simulation engine: GROMACS 2019.5</p> <p>Temperature: 314 K</p>
MD simulation of DMPC bilayer with CHARMM36 force field. Full hydration
<p>MD simulation of DMPC bilayer with CHARMM36 force field. Full hydration</p> <p>Dataset contains simulation files including trajectories (.xtc) (original production.xtc, and equilibrated and centered ).</p> <p>System: DMPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 10000</p> <p>Simulation time: 500 ns</p> <p>Sampling rate: every 10 ps</p> <p>Simulation engine: GROMACS 2019.5</p> <p>Temperature: 314 K</p>
MD simulation of DMPC bilayer with CHARMM36 force field. 5 w/l.
<p>MD simulation of DMPC bilayer with CHARMM36 force field. 5 w/l.</p> <p>Dataset contains simulation files including trajectories (.xtc) (original production.xtc, and equilibrated and centered centered_pbcmol-20-500ns.xtc).</p> <p>System: DMPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 1000</p> <p>Simulation time: 1000 ns</p> <p>Simulation engine: GROMACS 2019.5</p> <p>Temperature: 314 K</p>
MD simulation of POPC bilayer with OPLS4 force field. 7.5 w/l.
<p>MD simulation of POPC (1-palmitoyl-2-oleoyl-phosphatidylcholine) bilayer with OPLS4 force field. 7.5 w/l</p> <p>Dataset contains original desmond trajectories (_trj), topologies (-out.cms), input files (.cfg, .msj, .cms), and other files</p> <p>For the ease of the upload, trajectory files (_trj) are divided to 250ns pieces and tarred (named desmond_md_popc7.5wl_opls4_x-xns_trj.tar.gz)</p> <p>Dataset also contains Gromacs converted files (.xtc, .gro and .top) </p> <p>System: POPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 1500</p> <p>Simulation time: 500 ns</p> <p>Simulation engine: Desmond 2022-2</p> <p>Temperature: 300 K</p>
MD simulation of POPC bilayer with OPLS4 force field. 10 w/l.
<p>MD simulation of POPC (1-palmitoyl-2-oleoyl-phosphatidylcholine) bilayer with OPLS4 force field. 10 w/l</p> <p>Dataset contains original desmond trajectories (_trj), topologies (-out.cms), input files (.cfg, .msj, .cms), and other files</p> <p>For the ease of the upload, trajectory files (_trj) are divided to 250ns pieces and tarred (named desmond_md_popc10_opls4_x-xns_trj.tar.gz)</p> <p>Dataset also contains Gromacs converted files (.xtc, .gro and .top) </p> <p>System: POPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 2000</p> <p>Simulation time: 500 ns</p> <p>Simulation engine: Desmond 2022-2</p> <p>Temperature: 300 K</p>
MD simulation of POPC bilayer with OPLS4 force field. 20 w/l
<p>MD simulation of POPC (1-palmitoyl-2-oleoyl-phosphatidylcholine) bilayer with OPLS4 force field. 20 w/l</p> <p>Dataset contains original desmond trajectories (_trj), topologies (-out.cms), input files (.cfg, .msj, .cms), and other files</p> <p>For the ease of the upload, trajectory files (_trj) are divided to 250ns pieces and tarred (named desmond_md_popc20_opls4_x-xns_.tar.gz)</p> <p>Dataset also contains Gromacs converted files (.xtc, .gro and .top) </p> <p>System: POPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 4000</p> <p>Simulation time: 500 ns</p> <p>Simulation engine: Desmond 2022-2</p> <p>Temperature: 300 K</p> <p> </p>
GROMACS Coordinates and force field files for the SC lipid barrier
Open the record for dataset details and reuse information.
Amyloid-beta 16-22 peptide monomer simulation with the CHARMM-Drude force field and OpenMM (Run 2)
<p>Amyloid-beta 16-22 peptide (monomer) simulations with the CHARMM-Drude force field and OpenMM. This is the second independent simulation runs out of 3.</p> <p>Part 1-2 are 200 ns long, 3-8 are 100 ns each. Total trajectory length is 1 microseconds. Frame saving frequency is 10 ps.</p> <p>The system contains ~ 150 mM NaCl.</p>
Amyloid-beta 16-22 peptide monomer simulation with the CHARMM-Drude force field and OpenMM (Run 3)
<p>Amyloid-beta 16-22 peptide (monomer) simulations with the CHARMM-Drude force field and OpenMM. This is the last independent simulation runs out of 3.</p> <p>Part 1-2 are 200 ns long, 3-8 are 100 ns each. Total trajectory length is 1 microseconds. Frame saving frequency is 10 ps.</p> <p>The system contains ~ 150 mM NaCl.</p>
Amyloid-beta 16-22 peptide monomer simulation (without salt) with the CHARMM-Drude force field and OpenMM (Run 1)
<p>Amyloid-beta 16-22 peptide (monomer) simulations with the CHARMM-Drude force field and OpenMM. Initial structures are obtained from CHARMM-GUI. This is the first independent simulation runs out of three. The system does not contain any ions.</p> <p>Total trajectory length is 1 microseconds. Frame saving frequency is 10 ps.</p> <p>All the simulation parameters and force field files are uploaded into this repository. Simulations are done with OpenMM v. 7.5.1.</p> <p> </p>
Amyloid-beta 16-22 peptide dimer simulation (150 mM NaCl) with the CHARMM-Drude force field and OpenMM (Run 2)
<p>MD simulations of the Amyloid-beta 16-22 dimer at 150 mM NaCl concentration with CHARMM-Drude force field and OpenMM. Initial structure is obtained from CHARMM-GUI. In the initial configuration, two amyloid-beta 16-22 monomers are not interacting. This repository contains the second out of three independent runs.</p> <p>All the simulation parameters and force field files are uploaded into this repository. Simulations are done with OpenMM v. 7.5.1.</p> <p>The trajectory is divided into 7 parts: part_1-2 are each 200 ns long; part_3-6 are each 100 ns long, and part_7 is 640 ns long. Frames are saved in every 10 ps.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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.