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53 results for “simulation input files”
Dipolar Relaxation of Water Protons in the Vicinity of a Collagen-Like Peptide: Input Files for Simulation
<p>Input files to run the simulations in the paper</p> <p>Journal: The Journal of Physical Chemistry B<br> Title: Dipolar relaxation of water protons in the vicinity of a collagen-like peptide<br> Authors: Jouni Karjalainen, Henning Henschel, Mikko J. Nissi, Miika T. Nieminen, Matti Hanni<br> DOI: 10.1021/acs.jpcb.2c00052</p>
Raw data and simulation input file for friction experiment "crack28" performed at Geoazur on 2023/06/30.
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Molecular dynamics simulation input files: Dynamics of amphiphilic poly($\varepsilon$-caprolactone) micelles with doxorubicin and transition temperature predictions using all-atom molecular dynamics simulation
<p>The files uploaded contain the input files for simulations:<br><br>1) P10_Solv: Input files for drug-free micelles.<br>2) Micelle_Solv: Input files for drug-loaded micelles.</p>
Simulation input files: Cargo Release from Non-enveloped Viruses and Virus-like nanoparticles: Capsid Rupture or Pore Formation
<p>Simulation input files, and code for modification to simulation software for article:</p> <p>Cargo Release from Non-enveloped Viruses and Virus-like nanoparticles: Capsid Rupture or PoreFormation</p> <p>Lukáš Sukeník,†,‡</p> <p>Liya Mukhamedova,†</p> <p>Michaela Procházková,†</p> <p>Karel Škubník,†</p> <p>Pavel Plevka,†</p> <p>and Robert Vácha∗,†,‡,¶</p> <p>†CEITEC – Central European Institute of Technology, Masaryk University, Kamenice753/5, 625 00 Brno, Czech Republic</p> <p>‡Department of Condensed Matter Physics, Faculty of Science, Masaryk University,Kotl ́aˇrsk ́a 267/2, 611 37 Brno, Czech Republic</p> <p>¶National Centre for Biomolecular Research, Faculty of Science, Masaryk University,Kamenice 5, 625 00 Brno, Czech Republic</p> <p>E-mail: robert.vacha@mail.muni.cz</p>
Molecular dynamics simulation input files: Histone Tail Electrostatics Modulate E2-E3 Enzyme Dynamics: A Gateway to Regulate Ubiquitination Machinery
<p>Molecular dynamics simulation input files: Histone Tail Electrostatics Modulate E2-E3 Enzyme Dynamics: A Gateway to Regulate Ubiquitination Machinery (<a href="https://zenodo.org/record/7423328">https://zenodo.org/record/7423328</a>)</p>
Input files to run the Iquitos dengue simulator
<p>Input files to run the Iquitos dengue simulator</p>
Input files and setup for simulations of ancestral and modern glycosidases
<p>Input files, heme parameters, and representative structures from simulations of ancestral glycosidases and the modern glycosidase from the thermophilic <em>Halothermothrix orenii</em>. For details please see the README file provided.</p>
HemeLB input files for areteriovenous fistula simulation
<p>This dataset contains the HemeLB input files used to run the blood flow simulations described in our manuscript "High fidelity physiological blood flow in patient-specific arteriovenous fistula for clinical applications". These work with the PressureCouplingBeds and ResistorCapacitorBeds branches of the source code available at https://github.com/UCL-CCS/HemePure_SelfCoupled.</p> <p>Provided in this dataset are four *.tar.gz files containing the necessary input files for the flow simulations through the arteries and veins of the left forearm discussed in our manuscript: 1) Healthy vessels, 2) Arteriovenous fistula via modified mapping, 3) End-to-Side arteriovenous fistula and 4) Side-to-Side arteriovenous fistula. The files for 1), 3) and 4) contain the *.gmy files, input *.xml files for arteries and veins, the *0to1.txt map files describing the mapping parameters for the capillaries beds of the models and the MESH* files used to construct velocity boundary conditions for the geometry inlets. The *.gmy and MESH* files for 1) are reused for 2) in conjunction with the input* and *0to1.txt map files provided for 2). When launching the jobs, all relevant files are called from the input *.xml files - those labelled PCB are to be used with the PressurCoupling Beds branch and the those labelled RC with the ResistorCapacitorBeds branch.</p>
Input and output files for WRF urban simulations for the metropolitan area of Tel-Aviv
<p><span><span>We implement and verify for the first time four Weather Research and Forecasting model urban configurations, </span></span><span><span>focused on the coastal metropolitan area of Tel-Aviv (MTA) using updated land use and morphological maps. We analyze the mesoscale summertime flow and the urban canopy (UC) role in the occurrence of different hodograph dynamics observed within MTA at night. These events may be significant in air quality research. The four configurations – bulk (MM), single-layer (SLUCM), multi-layer (BEP), and BEP coupled with the building energy model – reproduce the observed diurnal temperature and wind cycles, with similar 10m wind direction bias and RMSE (15<sup>o</sup> and ~30<sup>o</sup>, respectively), with preference for MM and SLUCM at night. However, the SLUCM shows the lowest skill for the 10m wind speed (WS) (bias and RMSE 1ms<sup>-1</sup>), and the BEP shows the largest underestimation of the 2m temperature, ~-2.5<sup>o</sup>C. In the SLUCM, the WS increases over an UC and with increasing building heights. These results call for a re-examination of the SLUCM WS parameterization. The simulations show that at night, a convergence line (CL) builds up with the urban heat island, downstream of the NW flow. West of the CL, the wind continues flowing from the sea, and rotates anti-clockwise to form a non-elliptical sea-breeze hodograph. Removing MTA UC restores an elliptical hodograph. East of the CL, the UC supports an elliptical hodograph with a clockwise rotation through the NE sector, previously reported as dynamically unstable. We expect such wind hodograph dynamics within similar coastal metropolitan areas.</span></span></p>
Wildland-urban interface fire dynamics simulator input files for pyric tree spatial patterning interactions in historical and contemporary mixed conifer forests, California, USA
<p><span>Tree spatial patterns in dry coniferous forests of the western US, and analogous ecosystems globally, were historically aggregated, comprising a mixture of single trees and groups of trees. Modern forests, in contrast, are generally more homogeneous and overstocked than their historical counterparts. As these modern forests lack regular fire, pattern formation and maintenance is generally attributed to fire. Accordingly, fires in modern forests may not yield historically analogous patterns. However, direct observations on how selective tree mortality among pre-existing forest structure shapes tree spatial patterns is limited. In this study, we (1) simulated fires in historical and contemporary counterpart plots in a Sierra Nevadan mixed-conifer forest, (2) estimated tree mortality, and (3) examined tree spatial patterns of live trees before and after fire, and of fire-killed trees. Tree mortality in the historical period was clustered and density-dependent, because trees were aggregated and segregated by tree size before fire. Thus, fires maintained an aggregated distribution of tree groups. Tree mortality in the contemporary period was widespread, except for dispersed large trees, because most trees were a part of large, interconnected tree groups. Thus, post-fire tree patterns were more uniform and devoid of moderately sized tree groups. Post-fire tree patterns in the historical period, unlike the contemporary period, were within the historical range of variability identified for the western US. This divergence suggests that decades of forest dynamics without significant disturbances has altered the historical means of pyric pattern formation. Our results suggest that ecological silvicultural treatments, such as forest restoration thinnings, which emulate qualities of historical forests may facilitate the reintroduction of fire as a means to reinforce forest structural heterogeneity.</span></p>
West Atlantic simulation input files and run
<p>Dataset to reproduce runs in Irrmann, G. et al.: <em>Improving Ocean Modelling Software NEMO 4.0 benchmarking and communication efficiency</em>, Geosci. Model Dev (https://doi.org/10.5194/gmd-15-1-2022).</p> <p><a href="https://zenodo.org/api/files/fdfef221-a04f-49bc-8bdb-5a7e84c0e989/IAS24_light.tar?versionId=b6e40319-d3c9-4b56-a2eb-f406f11b4ed2">IAS24_light.tar</a> contains input files needed to reproduce runs of the West Atlantic simulation.</p> <p><a href="https://zenodo.org/api/files/fdfef221-a04f-49bc-8bdb-5a7e84c0e989/19940101_19940103.tar?versionId=ea8757ef-65ce-4fd5-9f90-86122bf22117">19940101_19940103.tar</a> is an example of a run of the West Atlantic simulation, the <em>timing.output </em>file contains data to reproduce a plot of computing time per time step.</p>
Simulation input files and analysis scripts for "Small ionic radii limit time step in Martini 3molecular dynamics simulations"
<p>Simulation input files and analysis scripts for "Small ionic radii limit time step in Martini 3molecular dynamics simulations".</p> <p>See <a href="https://aip.scitation.org/doi/10.1063/5.0095523">https://aip.scitation.org/doi/10.1063/5.0095523</a> for details.</p> <p>NOTE: some combinations of settings result in simulations that crash!<br> </p>
Input files for WRF simulations Across the the iCMV
<p>The west-east terrain cross-section along ~150km of the northern part of Israel has a coastal-plain—mountain—valley structure; hereafter denoted iCMV. The boundary layer height (BLH) evolution mechanism across the iCMV has not yet been fully understood. We use Weather Research and Forecasting (WRF) simulations and ceilometer measurements to decipher the iCMV BLH evolution mechanism during the late summertime period of 5-14 September 2017, where the daily maximum BLH at the mountainous city of Jerusalem (JrM; 800m above sea-level) varies by ~1000m. We first verify the BLH, simulated by 5 model configurations (with 4 different BL schemes). The RMSE for the 3 best configurations are around 160 and 200m for the coastal and JrM areas, respectively. An analysis of the simulated daily BL evolution reveals a general mechanism. In the early morning, the up-slope flows and synoptic forcing interact to induce a surface flow convergence (SFC) zone. During a westerly (easterly) synoptic flow, the SFC is induced east (west) of JrM. Assisted by the inland propagating sea breeze front, the SFC is advected eastwards during the afternoon, until it collapses at the valley bottom. The SFC zone is accompanied by a <a name="_Hlk110946754"></a>substantial positive vertical-wind column and a locally-elevated BLH. The more western the morning-time SFC is, the more likely the elevated BLH will pass during midday through JrM, with a higher daily maximum BLH. The exact dependence of the BLH evolution and the associated temperature and humidity variations upon the synoptic regime require further study.</p>
Simulation input files and analysis scripts for "Optimal bond-constraint topology for molecular dynamics simulations of cholesterol"
<p>Simulation input files and analysis scripts for "Optimal bond-constraint topology for molecular dynamics simulations of cholesterol".</p> <p>See ... for details.</p>
Input files for molecular dynamics simulations of holo CaM tagged with Alexa Fluor 488 and Texas Red dyes using Amber20
<p>Here we share the input files for molecular dynamics simulations of holo CaM tagged with Alexa Fluor 488 and Texas Red dyes using Amber20, as well as the TrESP charges used in TrESP-MMPol electronic coupling calculations of FRET properties. Links to the TrADA tool used to derive TrESP charges and the Trespcoup software used to compute electronic couplings for FRET are indicated below:</p> <div> <div> <div> <p>Cupellini, L., Jurinovich, S., & Mennucci, B. (2024). TraDA - Transition Density Analyzer. Zenodo. https://doi.org/10.5281/zenodo.10966411</p> <p>Cupellini, L., Lipparini, F., & Cignoni, E. (2024). trespcoup - Software to compute TrEsp couplings. Zenodo. https://doi.org/10.5281/zenodo.10966391</p> </div> </div> </div>
"Laser wakefield accelerator driven by the super-Gaussian laser beam in the focus" - Input files for the PIC simulations in the EPOCH Code
<p>These are particle-in-cell simulation set-ups for the EPOCH code. The simulations show the super-Gaussian beam diffraction in free space and in plasma (LWFA acceleration).</p> <p>Coresponding publication is currently reviewed.</p>
Input files for MD simulations of VP40 matrix protein dimer-dimer structure for WT, G198R, and G201R
<p>For AA simulations, the inp files need to have the path for the toppar folder and the corresponding pdb/psf files need to be renamed.</p>
MD simulation input files and results for ,,Atomistic MD simulations of n-alkanes in a phospholipid bilayer: CHARMM36 versus Slipids"
<p>Input files and trajectories of n-alkane/lipid systems used in the article: ,,Atomistic MD simulations of n-alkanes in a phospholipid bilayer: CHARMM36 versus Slipids".</p> <p>Equilibrated starting configurations were created using CHARMM36. Otherwise, filenames specifiy the force field used (C36 or SL), Temperature and system composition.</p> <p>.xtc trajectories were created using gmx trjconv with options -pbc nojump -dt 10. run2 equals simulations from 100-200ns, run3 equals 200-300ns. The first 100ns were excluded from the analysis and are not included in this dataset.</p> <p>Exemplary .mdp files have been included for both force-fields. Please refer to the manuscript for the force field sources and additional information.</p>
Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations: Simulations Topology, Coordinate, Parameters, Input and Output files
<p>The simulation data for the article: Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations.</p> <p>ck_metad.tar.gz: Includes the topology files, coordinates files and gromacs parameter input file (.mdp) used for WT-MetaD-HREX simulations with different c(K+), which are newly added runs for resubmission. The corresponding script files and Plumed files are in GitHub.</p> <p>eq_mini.tar.gz: Includes the parameter files required for the equilibration and minimization protocol.</p> <p>standard_md.tar.gz: Includes the topology files and coordinate files for all systems built in the article. Also include the hbfix parameters file required on the MD run, and the MD script file.</p> <p>metad.tar.gz: Includes the topology files, coordinates files and gromacs parameter input file (.mdp) used for WT-MetaD-HREX simulations. The corresponding script files and Plumed files are in GitHub.</p> <p>metad*fe*.tar.gz: Plumed HILLS files and metad.bias data used for drawing the free energy landscapes.</p> <p>ions.tar.gz: Data used for Figure.3 in the manuscript</p> <p>si_data.tar.gz: All data used for SI figures.</p>
Input files for Húsavík-Flatey Fault Zone dynamic simulations
<p>This repository contains the input files needed to reproduce the simulations shown in the paper "<a href="https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2022JB025886">Dynamic rupture models, fault interaction and ground motion simulations for the segmented Húsavík‐Flatey Fault Zone, Northern Iceland</a>"</p>
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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.