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1,670 results for “FORCE”
POPC @ 310K, Slipids force field.
<p>Input parameter file and part of the resulting trajectory for a POPC bilayer simulation using the Slipids force field [1,2]. Initial structure, force field parameters and simulation parameters were taken from the Slipids web page (http://people.su.se/~jjm/Stockholm_Lipids/Downloads.html). The structure simulated at 303K was used (http://people.su.se/~jjm/Stockholm_Lipids/Downloads_files/POPC_303K.gro)</p> <p>This data is used in the project "Matching lipid force fields with NMR data", see: http://nmrlipids.blogspot.fi.</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>Files:</p> <p>md.tpr – run input file for Gromacs versions 4.6 and above</p> <p>md.xtc – The last 150 ns of a 200 ns long simulation. Data saved every 100 ps.</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>[1] Joakim P. M. Jämbeck, Alexander P. Lyubartsev. <strong>Derivation and Systematic Validation of a Refined All-Atom Force Field for Phosphatidylcholine Lipids</strong>, <em>J. Phys. Chem. B, 2012, 116 (10), 3164-3179</em></p> <p>[2] Joakim P. M. Jämbeck, Alexander P. Lyubartsev. <strong>An Extension and Further Validation of an All-Atomistic Force Field for Biological Membranes</strong>, <em>J. Chem. Theory Comput., 2012, 8 (8), 2938-2948 </em></p>
Simulation files for DPPC lipid membrane with Slipids force field for Gromacs MD simulation engine
<p>The goal was to study the effect of salt on the order <br /> parameters of the lipid head group and the glycerol <br /> backbone for the NMRlipids project, see <br /> http://nmrlipids.blogspot.fi for more information.</p>
Simulation files for POPC lipid membrane with Charmm36 force field without NBFIX for Gromacs MD simulation engine
<p>Simulation files for POPC lipid membrane with Charmm36 force field without NBFIX for Gromacs MD simulation engine</p> <p>NaCl concentration is 730 mM.</p> <p>The goal was to study the effect of salt on the order <br /> parameters of the lipid head group and the glycerol <br /> backbone for the NMRlipids project, see <br /> http://nmrlipids.blogspot.fi for more information.</p>
Simulation files for DPPC lipid membrane with Slipids force field for Gromacs MD simulation engine
<p>the files denoted with 350 resp 700 resp 1000 have NaCl concentrations of 850 resp 1750 resp 2570 mM.</p> <p> </p> <p>The goal was to study the effect of salt on the order parameters of the lipid head group and the glycerol backbone for the NMRlipids project, see http://nmrlipids.blogspot.fi for more information.</p>
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>
Data and code for the manuscript "Internal vs Forced Variability Metrics for General Circulation Models Using Information Theory"
<p>Data and code for the manuscript "Internal vs Forced Variability Metrics for General Circulation Models Using Information Theory" published in the Journal of Geophysical Research Oceans. <br>URL of the manuscript: https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2023JC020101<br>DOI of the manuscript: https://doi.org/10.1029/2023JC020101</p>
CICE JRA55 Forcing on tx1 grid by year. 2023-09-19
<p>The JRA55 forcing on the tx1 grid broken out by year.</p><p>There was a bug found in the previous version and this is the updated fixed version.</p>
AFM data of ice clusters on Cu(111) and Au(111) in paper "Structure discovery in Atomic Force Microscopy imaging of ice"
<p>Frequency shift CO-tip atomic force microscopy data of small ice clusters on Cu(111) and Au(111) surfaces as they appear in the paper "Structure discovery in Atomic Force Microscopy imaging of ice".</p><p>The data are saved in a compressed .tar.gz archive. The unpacked archive contains each experiment as a Numpy .npz file. Each file contains the measurement data as a 3D array in the key 'data' and the physical extent of the scan region in the x and y directions in Ånströms in the keys 'lengthX' and 'lengthY'.</p>
Tunable force transduction through the Escherichia coli cell envelope
<p>Killing Assays, SDS Assays, Microscopy profiles and segmented cells (.res files for MicrobeJ).</p>
Table 8 for the Study: "Correlation Study: Triggering and Magnitude of Earthquakes in Italy (≥M4.3) in Relation to the Positions and Gravitational Forces of the Sun, Moon, and Planets Relative to Earth."
<p>Summary distribution and probability graphs for the study: <i>"Correlation Study: Triggering and Magnitude of Earthquakes in Italy (≥M4.3) in Relation to the Positions and Gravitational Forces of the Sun, Moon, and Planets Relative to Earth". </i>Summary distribution and probability of the three σFR indices (parameters A, B and % Alert Time) of the Hypothesis 2 for all 200 earthquakes, for Section 3.2.2.</p>
Table 6 for the Study: "Correlation Study: Triggering and Magnitude of Earthquakes in Italy (≥M4.3) in Relation to the Positions and Gravitational Forces of the Sun, Moon, and Planets Relative to Earth."
<p>Summary Excel tables for the study: <i>"Correlation Study: Triggering and Magnitude of Earthquakes in Italy (≥M4.3) in Relation to the Positions and Gravitational Forces of the Sun, Moon, and Planets Relative to Earth". </i>Results of the first hypothesis, for both the sample of 200 and the 63 earthquakes that occurred after 1988, for Section 3.1.</p>
Table 7 for the Study: "Correlation Study: Triggering and Magnitude of Earthquakes in Italy (≥M4.3) in Relation to the Positions and Gravitational Forces of the Sun, Moon, and Planets Relative to Earth."
<p>Summary graphs for the study: <i>"Correlation Study: Triggering and Magnitude of Earthquakes in Italy (≥M4.3) in Relation to the Positions and Gravitational Forces of the Sun, Moon, and Planets Relative to Earth". </i>Data distributions of the Hypothesis 2, with the R² regression coefficients of the three σFR values and indices (parameters A, B and % Alert Time) of both the 200 earthquakes and the 63 earthquakes after 1988, for Section 3.2.1.</p><p>The R² regression coefficients of each curve are calculated in the Excel files on the 2 Drives: </p><p>https://docs.google.com/spreadsheets/d/17UGHZlvZ2N-g6TOzgqpIe248_IitBmka8DbGWsv-lKQ/edit?usp=sharing, for the 200 earthquakes.</p><p>https://docs.google.com/spreadsheets/d/1Pyd4wZxZrq6G76nM2SwHYBBjbPZz7uM8GeO7PXG7obU/edit?usp=sharing, for the 63 earthquakes after 1988.</p>
Table 9 for the Study: "Correlation Study: Triggering and Magnitude of Earthquakes in Italy (≥M4.3) in Relation to the Positions and Gravitational Forces of the Sun, Moon, and Planets Relative to Earth."
<p><strong>Overview of the 200 analyzed earthquakes encompassing values and indices for σFR Parameters A, B, and the percentile of Alert Time across the three Analysis Lines, for Section 3.2.6.</strong></p><p>It contains 1 Excel calculation file, consisting of 3 excel sheet for each of the 3 lines of analysis, for both the 200 earthquakes since 1600 and for the 63 earthquakes that occurred after 1988.</p>
SST forcing experiments
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Data and scripts used to produce the figures for state-dependent CO2 forcing paper
<p>Data and scripts used to produce the figures for state-dependent CO2 forcing paper (He et al., 2023)</p>
Dataset in csv format containing labor force data in a synthetic population
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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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Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
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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.