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Dataset results
64 results for “CaCl2”
MD simulation trajectory for Heterogenous lipid bilayer with 150mM CaCl2 concentration
<p>Equilibrated symmetric heterogenous lipid bilayer simulation ran with Gromacs 2020.4, Force field= Charmm36m, 300ns, T=300K, composed of 152 POPC, 96 POPE, 20 POPS, 80 CHOL, 36 PSM, and 16 GM1 molecules, 73 Ca2+, 110 Cl2- , 18915 water (TIP3P) molecules. </p>
Pure POPC Membrane with 450mM CaCl2 simulations using Drude Polarizable Force Field and OpenMM
<p>500 ns MD simulation of pure POPC membrane using Charmm-Drude polarizable force field. The system contains 128 POPC lipids, 52 CaCl2, and 6400 SWM4 water molecules. </p> <p>The simulation have been performed using OpenMM 7.4.1 Frames are saved in every 10 ps. 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. The first 100 ns of the Drude simulation has been discarded from this dataset.</p> <p>wrapped.dcd has a frame saving frequency of 100 ps.</p> <p><strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the wrapped_full.dcd trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "wrapped_full.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps. </strong></p> <p><strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong></p> <p><strong>This simulation consists of 5 sub-trajectories, each of which starts from the last frame of the previous one and runs for 100 ns. These trajectories (originally in dcd format) were centered with VMD command "pbc wrap -center origin -centersel lipid -compound residue -all", concatenated and saved in xtc format with MDAnalysis.</strong></p> <p> </p>
Identification of calcineurin-dependent, Crz1-independent gene expression changes in response to chronic CaCl2 stress
GEO Series GSE254552. Saccharomyces cerevisiae. 24 samples. Type: Expression profiling by high throughput sequencing.
A. fumigatus wild type strain transcriptome analysis upon 200 mM CaCl2 treatment.
GEO Series GSE9516. Aspergillus fumigatus. 2 samples. Type: Expression profiling by array.
Identification of calcineurin-dependent gene expression changes in response to chronic CaCl2 stress
GEO Series GSE254551. Saccharomyces cerevisiae. 24 samples. Type: Expression profiling by high throughput sequencing.
Transcriptome analysis of Aspergillus fumigatus delta crzA mutant upon 10 and 30 minutes treatment with CaCl2 (200 mM)
GEO Series GSE15432. Aspergillus fumigatus. 4 samples. Type: Expression profiling by array.
LIPID17 POPC-POPG 50:50 MD simulation, Na+ counterions and 1000mM CaCl2, 298K
<p>The last 200ns of 720ns of MD simulation trajectory with Amber lipid 17 force field. POPC-POPG 50:50 (150 POPC, 150 POPG) with Na+ counterions and 1000mM CaCl2. The starting structure and lipid 17 parameters from here: https://zenodo.org/record/2585523#.Xbf0FC17FBx The starting structure was generated by removing appropriate number of POPC lipids to get 50:50 ratio. Dihedral types are corrected to type 9 as discussed here: https://github.com/NMRLipids/NMRlipidsIVPEandPG/issues/12.</p>
LIPID17 POPC-POPG 50:50 MD simulation, Na+ counterions and 100mM CaCl2, 298K
<p>The last 198ns of a 718ns MD simulation trajectory with Amber lipid 17 force field. POPC-POPG 50:50 (150 POPC, 150 POPG) with Na+ counterions and 100mM CaCl2. The starting structure and lipid 17 parameters from here: https://zenodo.org/record/2585523#.Xbf0FC17FBx The starting structure was generated by removing appropriate number of POPC lipids to get 50:50 ratio. Dihedral types are corrected to type 9 as discussed here: https://github.com/NMRLipids/NMRlipidsIVPEandPG/issues/12.</p>
LIPID17 POPC-POPG 80:20 MD simulation, Na+ counterions and 1000mM CaCl2, 298K
<p>The last 200ns from a 1200ns MD simulation trajectory with Amber lipid 17. POPC-POPG 80:20 (POPC 350, POPG 88) with Na+ counterions and 1000mM CaCl2. The starting structure and lipid 17 parameters from here: https://zenodo.org/record/2585523#.Xbf0FC17FBx The starting structure was generated by removing appropriate number of POPG lipids to get 80:20 ratio. Dihedral types are corrected to type 9 as discussed here: https://github.com/NMRLipids/NMRlipidsIVPEandPG/issues/12.</p>
POPC:POPG 4:1 MD simulation with CHARMM36 in 0.1 M CaCL2 solution with Na+ counter ions
<p>CHARMM36 POPC:POPG 4:1 bilayer simulation in 0.1 M CaCl2 solution. The initial structure was taken from CHARMM-GUI. Temperature is 298 K. The system contains 350 POPC, 88 POPG, 88 sodium ions, 26280 TIP3 water molecules, 47 Ca2+ ions and 94 Cl- ions.</p> <p>Total length of simulation is 400 ns. First 100 ns were discarded. Saving frequency of 100-300ns.xtc is 20 ps.</p>
POPC:POPG 4:1 MD simulation with CHARMM36 in 1 M CaCL2 solution with Na+ counterions
<p>CHARMM36 POPC:POPG 4:1 bilayer simulation in 1 M CaCl2 solution. The initial structure was taken from CHARMM-GUI. Temperature is 298 K. The system contains 350 POPC, 88 POPG, 88 sodium ions, 24927 TIP3 water molecules, 451 Ca2+ ions and 902 Cl- ions.</p> <p>Total length of simulation is 400 ns. First 100 ns were discarded as equilibration time. Saving frequency of 100-300ns.xtc is 20 ps.</p>
Lipid17ecc POPC:POPG 4:1 bilayer simulation in 0.1 M CaCl2 solution and Na+ counter ions
<p>Lipid17ecc POPC:POPG 4:1 bilayer simulation in 0.1 M CaCl2 solution. The initial structure was taken from https://zenodo.org/record/3833725#.X0OayxmEZGG . Temperature is 298 K. The system contains 350 POPC, 88 POPG, 88 Na+ ions, 26124 SPCE water molecules, 47 Ca2+ ions and 94 Cl- ions</p> <p>Total length of simulation is 400 ns. First 100 ns were discarded as equilibration time. Saving frequency of 100-300ns.xtc is 20 ps.</p>
MD simulation of POPC bilayer with OPLS3e force field, 200 mM CaCl2 part 2
<p>MD simulation of POPC bilayer with OPLS3e force field, 200 mM CaCl<sub>2</sub> part 2 (500-1000ns)</p> <p>Dataset contains trajectories (_trj) for the last 500ns of the 1000ns trajectory, topology (-out.cms), and other files</p> <p>For the ease of the upload, trajectory files (_trj) are divided to 100ns pieces and tarred (named desmond_md_cacl200_x-xns.tar.gz)</p> <p>System: POPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 8880</p> <p>Salt: CaCl<sub>2</sub></p> <p>Concentration: 200 mM</p> <p>Number of cations: 32</p> <p>Simulation time: 1000 ns (in this dataset 500-1000ns)</p> <p>Simulation engine: Desmond 2019-4</p> <p>Temperature: 300 K</p> <p>Related dataset: MD simulation of POPC bilayer with OPLS3e force field, 200 mM CaCl<sub>2</sub> part 1</p>
MD simulation of POPC bilayer with OPLS3e force field, 50 mM CaCl2 part 2
<p>MD simulation of POPC bilayer with OPLS3e force field, 50 mM CaCl<sub>2</sub> part 2 (500-1000ns)</p> <p>Dataset contains trajectories (_trj) for the last 500ns of the 1000ns trajectory, topology (-out.cms), and other files.</p> <p>For the ease of the upload, trajectory files (_trj) are divided to 100ns pieces and tarred (named desmond_md_cacl50_x-xns.tar.gz)</p> <p>System: POPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 8880</p> <p>Salt: CaCl<sub>2</sub></p> <p>Concentration: 50 mM</p> <p>Number of cations: 8</p> <p>Simulation time: 1000 ns (in this dataset 500-1000ns)</p> <p>Simulation engine: Desmond 2019-4</p> <p>Temperature: 300 K</p> <p>Related dataset: MD simulation of POPC bilayer with OPLS3e force field, 50 mM CaCl<sub>2</sub> part 1</p>
MD simulation of POPC bilayer with OPLS3e force field, 1000 mM CaCl2 part 1
<p>MD simulation of POPC bilayer with OPLS3e force field, 1000 mM CaCl<sub>2</sub> part 1</p> <p>Dataset contains trajectories (_trj) for the first 500ns of the 1000ns trajectory, topology (-out.cms) and input files (.cfg, .msj, .cms).</p> <p>For the ease of the upload, trajectory files (_trj) are divided to 100ns pieces and tarred (named desmond_md_cacl1000_x-xns.tar.gz).</p> <p>Dataset also contains Gromacs converted files (.xtc, .gro and .top). Converted trajectories is also for the first 500 ns of 1000 ns, and are as 100 ns pieces for analysis since simulation did not equilibrate during 1000 ns.</p> <p>System: POPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 8880</p> <p>Salt: CaCl<sub>2</sub></p> <p>Concentration: 1000 mM</p> <p>Number of cations: 160</p> <p>Simulation time: 1000 ns (in this dataset 0-500ns)</p> <p>Simulation engine: Desmond 2019-4</p> <p>Temperature: 300 K</p> <p>Related dataset: MD simulation of POPC bilayer with OPLS3e force field, 1000 mM CaCl<sub>2</sub> part 2</p>
MD Simulation data for a pure DOPC bilayer (1000 mM CaCl2) with AMOEBA force field + OpenMM
<p>MD simulation data for the DOPC bilayer + 1000 mM CaCl2 with the AMOEBA-based force field developed by Li (<a href="https://doi.org/10.1080/00268976.2018.1436201">https://doi.org/10.1080/00268976.2018.1436201</a>).</p> <p>The simulation contains 72 DOPC lipids, 36 CaCl2 ions, and 2880 water molecules. The trajectory is 218,41 ns long (21841 frames with 10 ps saving frequency).</p> <p><strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the previously uploaded trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "unwrapped_all_fixed_dt.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps. </strong></p> <p><strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong></p> <p><strong>This simulation consists of 12 sub-trajectories, each of which starts from the last frame of the previous one. These trajectories (originally in dcd format) were concatenated and saved in xtc format with MDAnalysis.</strong></p> <p> </p>
MD Simulation data for a pure DOPC bilayer (450 mM CaCl2) with AMOEBA force field + OpenMM
<p>MD simulation data for the DOPC bilayer + 450 mM CaCl2 with the AMOEBA-based force field developed by Li (<a href="https://doi.org/10.1080/00268976.2018.1436201">https://doi.org/10.1080/00268976.2018.1436201</a>).</p> <p>The simulation contains 72 DOPC lipids, 16 CaCl2 ions, and 2880 water molecules. The trajectory is 218,41 ns long (21841 frames with 10 ps saving frequency).</p> <p><strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the previously uploaded trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "unwrapped_all_fixed_dt.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps. </strong></p> <p><strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong></p> <p><strong>This simulation consists of 12 sub-trajectories, each of which starts from the last frame of the previous one. These trajectories (originally in dcd format) were concatenated and saved in xtc format with MDAnalysis.</strong></p> <p> </p>
Clinical Effectiveness of the Calcium Chloride (CaCl2) Surface- Treated Orthodontic Mini Implant (OMI)
ClinicalTrials.gov study NCT06607536. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Microarray analysis of long noncoding RNAs in primary human keratinocytes in response to CaCl2 stimulation
GEO Series GSE212548. Homo sapiens. 12 samples. Type: Non-coding RNA profiling by array; Expression profiling by array.
Transcript levels of genes in both the wild type SN148 and the crz1/crz1 mutant with or without 0.2M CaCl2 treatment
GEO Series GSE123122. Candida albicans. 4 samples. Type: Expression profiling by high throughput sequencing.
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