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53 results for “simulation input files”
Input files for simulation of potassium channels using the AMOEBA polarizable force field
<p>This dataset contains input Tinker xyz and key files for the simulation of KcsA potassium channels in DOPC bilayer, a simple script for converting CHARMM pdb file to Tinker xyz file, and modified Tinker source code to support one-dimensional position restraints.<br> "params.tar.gz" contains a description of the force field modifications.<br> <br> To use "mod2", add the following lines to the key file.</p> <pre><code>#compatible with amoebabio18.prm polarize 5 1.4500 0.3900 3 polarize 11 1.4500 0.3900 9 polarize 3 1.7500 0.3900 1 5 7 50 225 227 polarize 9 1.7500 0.3900 1 7 11 50 225 227</code></pre> <p> </p>
Bubble/Foam Simulations for Malej et al. 2023, source codes, input files, matlab files, data files
<p><i>.F are source codes, *.m are matlab scripts for analysis and postprocessing, .txt are data files including bathymetry and data from sensitivity tests</i></p>
Example input files and output data for 1D hydrodynamic simulations of shock compressed iron
<p>Example input files and output data for 1D hydrodynamic simulations of shock compressed iron. Input files consists of 3 examples from the SIMEX github wiki page for a 50 micron CH ablator with 5 micro Fe foil (laser pulse is a 6 ns flat top pulse, 1064 nm with 0.3 TW/cm<sup>2</sup>). Output data are from Esther hydrocode in .txt format and the SIMEX opmd.h5 format.</p>
Binding Affinity Prediction Workflow - Simulation Input Files and Absolute Binding Free Energies
<p>The Binding Affinity Prediction (BAP) workflow calculates absolute binding free energies for protein-ligand complexes by taking their crystal structures, converting them into input files for molecular dynamics (MD) simulations with GROMACS after they have passed extensive quality checks, and analysing the resulting trajectories with the Generalised Born model of implicit solvation as implemented in gmx_MMPBSA to obtain the free-energy estimates. The workflow was designed for soluble proteins without post-translational modifications, co-factors and non-standard amino acids, and it has limited support for coordinated ions.</p> <p>For the dataset published here, the BAP workflow was run on the PDBbind 2020 (http://www.pdbbind.org.cn/index.php) refined set. This entry contains the MD simulation input files (BAPSimulationInputFiles.tar.gz) and the ABFE estimates (BAPBindingFreeEnergyEstimates.csv) obtained from four 250 ns trajectories for each complex. The MD simulations for more than 4000 complexes were run on the Leonardo supercomputer while the implicit-solvent calculations were carried out on Galileo, both operated by Cineca (Italy). The MD trajectories will be stored at Cineca for approx. 1 year after publication of this entry; contact Cineca's user support if you are interested in the trajectories.</p> <p>The README file describes how to reproduce the MD trajectories and the subsequent implicit-solvent calculations yielding the free-energy estimates. The workflow scripts can be downloaded from GitHub (https://github.com/LigateProject/Binding-Affinity-Prediction-workflow). The MD simulations were run with GROMACS 2023.2 (https://manual.gromacs.org/2023.2/index.html), and the implicit-solvent calculations were carried out with gmx_MMPBSA 1.6.1 (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/v1.6.1/).</p>
Input files for "Faster Simulations with a 5 fs Time Step for Lipids in the CHARMM Force Field"
<p>The performance of all-atom molecular dynamics simulations is limited by an integration time step of 2 fs, which is needed to resolve the fastest degrees of freedom in the system, namely, the vibration of bonds and angles involving hydrogen atoms. The virtual interaction sites (VIS) method replaces hydrogen atoms by massless virtual interaction sites to eliminate these degrees of freedom while keeping intact nonbonded interactions and the explicit treatment of hydrogen atoms. We have modified the existing VIS algorithm for most lipids in the popular CHARMM36 force field by increasing the hydrogen atom masses at regular intervals in the lipid acyl chains and obtained lipid properties and pore formation free energies in very good agreement with those calculated in simulations without VIS. Our modified VIS scheme enables a 5 fs time step resulting in a significant performance gain for all-atom simulations of membranes. The method has the potential to make longer time and length scales accessible in all-atom simulations of membrane–protein complexes.</p> <p>The file set contains individual lipid topologies for virtual interaction sites for standard CHARMM lipids, as well as a README file with instructions on how to implement the VIS algorithm for membranes or membrane-protein complexes</p> <p>Please Cite: <a href="//pubs.acs.org/doi/10.1021/acs.jctc.8b00267">10.1021/acs.jctc.8b00267</a></p> <p> </p>
Test Input and Output Files for Cloud Resolving Radar Simulator (CR-SIM) Version 4.0
<h2>Overview</h2> <p>The dataset includes input and output files for testing the Cloud-Resolving Radar Simulator (Oue et al. 2020) version 4.0. </p> <p>The following files are included:</p> <ul> <li>crsimtest1_inp_MP10.tar.gz includes input files for Test-1 with the microphysical option MP10</li> <li>crsimtest2_inp_MP50.tar.gz includes input files for Test-2 with the microphysical option MP50</li> <li>crsimtest3_inp_MP40.tar.gz includes input files for Test-3 with the microphysical option MP40</li> <li>crsimtest1_out_ref_MP10.tar.gz includes example output files for Test-1 with the microphysical option MP10</li> <li>crsimtest2_out_ref _MP50.tar.gz includes example output files for Test-2 with the microphysical option MP50</li> <li>crsimtest3_out_ref _MP40.tar.gz includes example output files for Test-3 with the microphysical option MP40</li> </ul> <p>Detailed descriptions are also available in the CR-SIM user guide (https://github.com/marikooue/CR-SIM/releases/tag/crsim-v4.0).</p>
Deliverable 1.1.1.1 BEL-Float project | Dataset containing the results of numerical simulations (motions, forces) of the operational performance analysis - Input files
<p>This dataset contains the parent input used to generate the simulation files of the DeepCwind OC4 semi-submersible combined with the 5MW NREL turbine for various wind and wave conditions. The basis of the OpenFAST input files are taken from <a href="https://github.com/OpenFAST/r-test/tree/main/glue-codes/openfast/5MW_OC4Semi_WSt_WavesWN">OpenFAST r-test GitHub repository (5MW_OC4Semi_WSt_WavesWN)</a> and adapted to simulate various wind and wave conditions. The turbulent wind field as the input to the InflowWind module is generated using <a href="https://www.nrel.gov/wind/nwtc/turbsim.html">TurbSim</a>. The simulations are performed on a modified version of OpenFAST v3.5.3 to which adaptation to the code is made to extract additional Morison drag output up to 16 cylindrical members. This adapted code is <a href="https://github.com/abkpribadi/openfast/tree/Morison_additional_output">uploaded on GitHub as a branch from a forked OpenFAST repository</a>. In total there are 1152 simulation results consists of 768 irregular waves and 384 regular waves cases. The complete dataset is divided into 9 sub-datasets, see "Related work" section. A report describing this dataset will be made available on BEL-Float project website by November 2024: https://www.owi-lab.be/bel-float.</p>
Input Files for Peptide Translocation Across Phospholipid Membranes Using Various Collective Variables and Martini Coarse-Grained Simulations
<p>Input files for publication: Ivo Kabelka, Radim Brožek, and Robert Vácha: Selecting Collective Variables and Free Energy Methods for Peptide Translocation Across Membranes, Journal of Chemical Information and Modeling, submitted</p>
Input files for paper Insertases Scramble Lipids: Molecular Simulations of MTCH2
<p>Input files for simulations in publication: Ladislav Bartoš, Anant K. Menon, and Robert Vácha: Insertases Scramble Lipids: Molecular Simulations of MTCH2<br> </p>
Example input files and Fe foil data for FEFF EXAFS simulations of Fe
<p>Feff input file containing Fe atomic positions, needed to run FEFF simulations of the EXAFS of Fe. The Demeter XAS analysis program files are also included (free software) : http://bruceravel.github.io/demeter/#about. These files can be used to simulate EXAFS of Fe using the FEFF software. This simulation is a building block for a future enhancement of the SIMEX (Simulation of Experiments) platform : https://github.com/eucall-software/simex_platform</p>
PALM Model System v 6.0 input and configuration files for coupled large eddy simulations of land surface heterogeneity effects and diurnal evolution of late summer and early autumn atmospheric boundary layers during the CHEESEHEAD19 field campaign
<p>Namelist, configuration and forcing files for the PALM Model System 6.0 revision number 21.10-rc.2 used for the numerical simulations Coupled Large Eddy Simulations of land surface heterogeneity induced atmospheric boundary layer response during the CHEESEHEAD19 field campaign.</p>
Input files for the MD simulations and free energy calculations for the article "Water Dissolved in a Variety of Polymers Studied by Molecular Dynamics Simulation and a Theory of Solutions"
<p>Article:<em> </em><a href="https://pubs.acs.org/doi/10.1021/acs.jpcb.1c04818">J. Phys. Chem. B. 125, 9357–9371 (2021) [DOI: 10.1021/acs.jpcb.1c04818]</a></p> <p>The structures of the homopolymers and copolymers simulated are shown in Figures 1 and S1 and Tables 2 and 3. All-atom MD simulation was carried out using GROMACS, and this repository provides the input files with the GAFF/RESP force and initial coordinate files. The free energy of water dissolution was obtained with <a href="https://sourceforge.net/projects/ermod/">ERmod</a>, and the input files for the free-energy calculations are also contained. See the README files for details.</p>
Model_Input_Files_and_Simulation_Output
<p>This provides the BioRT-HBV model input and output for the paper submission "As above, so below: the growing importance of water and carbon processes beneath soils in a warmer and drier climate".<br><br>Coal_Creek_Original: Input and Output files associated with the model calibrated to average DOC years; used for making Figures 3, 4, 5, 6, 7, and 8.<br><br>Coal_Creek_High: Input and Output files associated with the model calibrated to high DOC years; used for making Figure 4.</p> <p>Rxn_Implementation_Results: Output files associated with the model simulations that have Resp-SZ only, and Resp-SZ & Resp-DZ; used for making Figure 5.<br><br>Input files and output for the various numerical experiments, used in figure 9: Coal_Creek_DryandWet, Coal_Creek_DryYears, Num_Exp_HBVResults_and_precipchem_files, Num_Exp_output<br><br>HBV-BioRT-new_ver(1).zip : files for the BioRT-HBV model</p>
Scrutinizing the protein hydration shell from molecular dynamics simulations against consensus small-angle scattering data (Simulation input files)
<p>Simulation input files for gromacs to reproduce the data from the manuscript "Scrutinizing the protein hydration shell from molecular dynamics simulations against consensus small-angle scattering data" (submitted to Comm. Chem.)</p>
LUNAR: Automated input generation and analysis for reactive LAMMPS simulations input and output files
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Input files and scripts for creating PALM simulation input files on Mäkelänkatu in Helsinki, Finland
<p>Datasets and scripts to create input files for running PALM simulations around Mäkelänkatu, Helsinki. The dataset contains:</p> <ul> <li>input_data_to_palm: raster maps and final input files to be applied by PALM</li> <li>scripts: scripts used to create the input files</li> <li>source_data: source data for creating the input files</li> <li>user_code: PALM user code modifications</li> </ul> <p> </p>
Input files and simulation results for reactive two-phase transport calculations in a waste package with OGS6-MP-LT-Drum
<p>The folders contain the original input and output files for reactive two-phase flow calculations with OpenGeoSys6-MP-LT-drum (doi:10.5281/zenodo.4060885), as well as the GEM-Selektor V3.3 project for look-up table generation, state<br> files for Paraview, R-script and jupyter notebook files used for post-processing the simulation output, which were used for creating the results in:</p> <p>Huang, Y., Shao, H., Wieland, E. <em>et al.</em> Two-phase transport in a cemented waste package considering spatio-temporal evolution of chemical conditions. <em>npj Mater Degrad</em> <strong>5, </strong>4 (2021). https://doi.org/10.1038/s41529-021-00150-z</p>
Input data files for simulation: top_hat_cg_supg
Input data files for simulation: top_hat_cg_supg
POPC/Cholesterol (70:30) lipid membrane, 303K, Charmm36 force field through the use of Gromacs input files, simulation files and 100 ns trajectory for openMM simulation engine v7
<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 openMM simulation engine v7 and CHARMM36 additive force field parameters obtained from CHARMM-GUI input files [1]. Specifically, Gromacs file format provided by [1] was specifically used for this simulation.</p> <p>Conditions: T=303, 84 POPC and 36 Cholesterol molecules, 4800 tip3p waters, 100ns 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>
Revised TOPAS input files for the simulation of WAXS, SAXS and PDF
<p>TOPAS input files for discrete and low-dimensional structure models: (1) a benzene molecule, (2) a PbS quantum dot, (4) a hydroxyapatite nano-fibril and (5) turbostratic carbon</p> <p>TOPAS calculations can be performed with the blank data file or <em>yobs_eqn =1; min 0 max 157.5204 del 0.1</em></p> <p>the file path of the blank data file has to be updated</p> <p>models can be found at <a href="https://doi.org/10.5281/zenodo.8169025" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.8169025</a></p>
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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.