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220 results for “force fields”
OpenMM simulations of POPC using the CHARMM Drude2023 force field
<p>PSF, single CRD file, and DCD format trajectories for the final 200 ns of triplicate POPC simulations, from the publication</p> <p><strong>Drude Polarizable Lipid Force Field with Explicit Treatment of LongRange Dispersion: Parametrization and Validation for Saturated and Monounsaturated Zwitterionic Lipids</strong><br> Yalun Yu, Richard M. Venable, Jonathan Thirman, Payal Chatterjee, Anmol Kumar, Richard W. Pastor,*<br> Benoît Roux,* Alexander D. MacKerell, Jr.,* and Jeffery B. Klauda*</p> <p> https://doi.org/10.1021/acs.jctc.3c00203</p> <p>DCD file names indicate the lipid, replica number, and the time point of the final coordinate set in the file; each file has frames spaced at 10 ps over a 50 ns interval.</p> <p> </p>
OpenMM simulations of DOPC using the CHARMM Drude2023 force field
<p>The dataset contains a PSF, a formatted coordinate file (CRD), and DCD files with the final 200 ns from each of 3 replicate simulations from the paper</p> <p><strong>Drude Polarizable Lipid Force Field with Explicit Treatment of LongRange Dispersion:<br> Parametrization and Validation for Saturated and Monounsaturated Zwitterionic Lipids</strong><br> Yalun Yu, Richard M. Venable, Jonathan Thirman, Payal Chatterjee, Anmol Kumar, Richard W. Pastor,*<br> Benoît Roux,* Alexander D. MacKerell, Jr.,* and Jeffery B. Klauda*<br> https://doi.org/10.1021/acs.jctc.3c00203</p> <p><br> DCD file names indicate the lipid, replica number, and the time point of the final coordinate set in the file; each file has frames spaced at 10 ps over a 50 ns interval.</p>
Pure POPC membrane simulations with 1000 mM NaCl with the CHARMM-Drude2023 force field (OpenMM)
<p>220.14 ns MD simulation of pure POPC membrane using Charmm-Drude2023 polarizable force field (</p> <p><strong>Drude Polarizable Lipid Force Field with Explicit Treatment of LongRange Dispersion:<br> Parametrization and Validation for Saturated and Monounsaturated Zwitterionic Lipids</strong></p> <p><strong>)</strong></p> <p>.The system contains 128 POPC lipids, 115 NaCl, and 6400 SWM4 water molecules.</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. Frame saving frequency is 10ps. There are 22014 frames in this trajectory.</p>
Pure POPC membrane simulations with 350 mM CaCl2 with the CHARMM-Drude2023 force field (OpenMM)
<p>219.59 ns MD simulation of pure POPC membrane using Charmm-Drude2023 polarizable force field (</p> <p><strong>Drude Polarizable Lipid Force Field with Explicit Treatment of LongRange Dispersion:<br> Parametrization and Validation for Saturated and Monounsaturated Zwitterionic Lipids</strong></p> <p><strong>)</strong></p> <p>.The system contains 128 POPC lipids, 41 CaCl2, and 6400 SWM4 water molecules.</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. Frame saving frequency is 10ps. There are 21959 frames in this trajectory.</p>
Comparative Study of Molecular Mechanics Force Fields for β-peptidic Foldamers: Folding and Self-Association
<p>Molecular dynamics simulation input files and Python scripts used for preparing the runs and analyzing the trajectories.</p>
Single lipid component membrane bilayer MD with CHARMM36 force field, simulated with the CHARMM program
<p>Data for ten single component lipid bilayer simulations, with 3 files per lipid: a DCD file with coordinates, a PSF file describing the system, and a .zip file containing the starting coordinate set (CHARMM COOR format) and the other inputs used for the CHARMM simulations. Only the POPG system includes ions: Na+ to neutralize the lipids, and ca. 0.15 M NaCl.</p> <p>The DCD trajectory files contain coordinate sets stored at 0.1 ns intervals, <br> and are in the original CHARMM binary format.</p> <p>Lipid Nlpd Nwat ns<br> DLPC 648 25920 200<br> DMPC 648 16632 100<br> DOPC 648 21681 350<br> DOPE 648 21681 350<br> DPPC 648 19701 300<br> POPC 648 20178 200<br> POPE 720 23049 100<br> POPG 648 29160 200<br> PSM 648 18828 200<br> SDPE 648 25920 100</p> <p>"Mechanical properties of lipid bilayers from molecular dynamics simulation",<br> R. M. Venable, F. L. Brown and R. W. Pastor,<br> Chemistry and Physics of Lipids, 192 pp. 60-74 (2015). </p> <p>https://pubmed.ncbi.nlm.nih.gov/26238099/<br> https://www.sciencedirect.com/science/article/pii/S0009308415300190?via%3Dihub</p> <p> See also:</p> <p>"Identifying systematic errors in a power spectral analysis of simulated<br> lipid membranes"<br> Muhammed F. Ergüder, Markus Deserno<br> J. Chem. Phys. 154, 214103 (2021); doi: 10.1063/5.0049448<br> </p> <p> </p>
MD simulations of the Sec61/TRAP/ribosome complex Amber force fields
<p>Simulation data for the Sec61/TRAP/ribosome complex embedded in an ER membrane mimic. Simulations are performed using GROMACS and with the all-atom Amber family of force fields. The uploaded trajectory (xtc) contains the coordinates stored every 2 ns of the 2-µs-long simulations. The output energy file (edr), run input file (tpr), and the continue point (cpt) at 2 µs are provided. </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>
MD simulations of the Sec61/TRAP complex with the Martini 3 force field
<p>Simulation data for the Sec61/TRAP complex, the Sec61 complex, and the TRAP complex in a POPC membrane. Simulations are performed using GROMACS and with the coarse-grained Martini 3 force fields. The proteins are kept restrained in the simulations. The uploaded trajectories (xtc) contain the coordinates stored every 10 ns of the 20-µs-long simulations. The output energy files (edr), run input files (tpr), and the continue points (cpt) at 20 µs are provided. </p> <p>All required input files are also provided to regenerate the run input files: initial structures (gro), index files (ndx), topologies (top and itp), and the common 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>
Molecular dynamics simulation trajectories for the GB99dms implicit solvent force field
<p>Molecular dynamics simulation trajectories used in training and validating the GB99dms implicit solvent protein force field. See the paper:</p> <ul> <li>Greener JG. Differentiable simulation to develop molecular dynamics force fields for disordered proteins, <a href="https://doi.org/10.1039/D3SC05230C" target="_blank" rel="noopener">Chemical Science</a> 15, 4897-4909 (2024)</li> </ul> <p>For more information, including structure files for these trajectories, see https://github.com/greener-group/GB99dms.</p>
Capturing the interactions in the BaSnF$_4$ ionic conductor: a comparison of machine-learning potentials and polarizable force fields
<p>The current files contain all the original data for our work "Capturing the interactions in the BaSnF<sub>4 </sub>ionic conductor: a comparison of machine-learning potentials and polarizable force fields". </p>
Data for: Hierarchial motor adaptations negotiate failures during force field learning
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Different functional networks underlying human walking with pulling force fields acting in forward or backward directions
Open the record for dataset details and reuse information.
Supporting Information: Toward learned chemical perception of force field typing rules
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Simulation of POPC:POPE 1:1 membrane with the Slipids force field
<p>A POPC:POPE 1:1 bilayer with 100 lipids per leaflet is simulated for 300 ns using the Slipids model and Gromacs simulation engine version 2019.4. The trajectory (.xtc) is saved every 100ps. The simulation parameters (.mdp), the energy file (.edr), the continue point to extend the simulation (.cpt), the run input parameters (.tpr), and the final structure (.gro) are also given. The lipid topologies (.itp) are provided, and the Slipids force field is available at http://www.fos.su.se/~sasha/SLipids/</p>
Datasets associated with "Improving Small Molecule Force Fields by Identifying and Characterizing Small Molecules with Inconsistent Parameters"
<p>This provides associated datasets for a paper/preprint forthcoming soon, by Ehrman et al., "Improving small molecule force fields by identifying and characterizing small molecules with inconsistent parameters". A poster describing an earlier portion of the work is available at https://doi.org/10.5281/zenodo.3385278. The AllMolsAllData.csv.gz file provides a Pandas dataframe for the full set of molecules considered, as described in the paper, whereas the 25andunderarchive.tar.gz provides optimized geometries for 265,847 molecules with four or more difference flags.</p>
Slipids-2020 force field for lipid bilayer simulations
<p>Slipids-2020 force field for various lipids<br> -----------------------------------------------------</p> <p>Authors: Joakim Jämbeck, Inna Ermilova, Fredrik Grote, Alexander Lyubartsev<br> Department of Materials and Environmental Chemistry,<br> Stockholm University, Stockholm 10691 Sweden<br> e-mail: alexander.lyubartsev@mmk.su.se<br> 2012 - 2020</p> <p><br> Content:</p> <p>Slipids_2020.ff: directory containing the force field.<br> Included into the Gromacs topology file by: <br> #include "Slipids_2020.ff/forcefield.itp"</p> <p>itp_files: itp files for various lipids<br> boxes: equilibrated configurations for some lipid systems</p> <p>The force field can be used together with the AMBER-family FF for proteins and GAFF for small molecules</p> <p> </p>
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>
ScienceDex guides
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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
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.