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66 results for “ECC”
TPP binding to POPC membrane, CHARMM36-QMcharges-ECC, 416 mM, 298 K
<p>System info in README.yaml, including basic analysis - headgroup OP, averaged APL and repead distance, analysis performed only from eqilibrated part of the simulation, marked as "BINDINGEQ"</p> <p>here:</p> <p>FILES:<br> xtc:<br> NAME: [name]<br> SIZE: [MB]<br> MODIFIED: [yyyy-mm-dd time]<br> LENGTH: [ps]<br> SAVING_FREQUENCY: [ps]<br> BEGIN: [ps] - how much of the simulation was simulated before and is excluded</p>
TPP binding to POPC membrane, CHARMM36-QMcharges-ECC, 277 mM, 298 K
<p>System info in README.yaml, including basic analysis - headgroup OP, averaged APL and repead distance, analysis performed only from eqilibrated part of the simulation, marked as "BINDINGEQ"</p> <p>here:</p> <p>FILES:<br> xtc:<br> NAME: [name]<br> SIZE: [MB]<br> MODIFIED: [yyyy-mm-dd time]<br> LENGTH: [ps]<br> SAVING_FREQUENCY: [ps]<br> BEGIN: [ps] - how much of the simulation was simulated before and is excluded</p>
TPP binding to POPC membrane, CHARMM36-QMcharges-Literature-ECC, 416 mM, 298 K
<p>System info in README.yaml, including basic analysis - headgroup OP, averaged APL and repead distance, analysis performed only from eqilibrated part of the simulation, marked as "BINDINGEQ"</p> <p>here:</p> <p>FILES:<br> xtc:<br> NAME: [name]<br> SIZE: [MB]<br> MODIFIED: [yyyy-mm-dd time]<br> LENGTH: [ps]<br> SAVING_FREQUENCY: [ps]<br> BEGIN: [ps] - how much of the simulation was simulated before and is excluded</p>
TPP binding to POPC membrane, CHARMM36-QMcharges-ECC, 138 mM, 298 K
<p>System info in README.yaml, including basic analysis - headgroup OP, averaged APL and repead distance, analysis performed only from eqilibrated part of the simulation, marked as "BINDINGEQ"</p> <p>here:</p> <p>FILES:<br> xtc:<br> NAME: [name]<br> SIZE: [MB]<br> MODIFIED: [yyyy-mm-dd time]<br> LENGTH: [ps]<br> SAVING_FREQUENCY: [ps]<br> BEGIN: [ps] - how much of the simulation was simulated before and is excluded</p>
Etidocaine binding to POPC membrane, CHARMM36-ParamChem-ECC, 138 mM, 298 K
<p>System info in README.yaml, including basic analysis - headgroup OP, averaged APL and repead distance, analysis performed only from eqilibrated part of the simulation, marked as "BINDINGEQ"</p> <p>here:</p> <p>FILES:<br> xtc:<br> NAME: [name]<br> SIZE: [MB]<br> MODIFIED: [yyyy-mm-dd time]<br> LENGTH: [ps]<br> SAVING_FREQUENCY: [ps]<br> BEGIN: [ps] - how much of the simulation was simulated before and is excluded</p>
Simulations of a POPC lipid bilayer in water solution at various NaCl and CaCl2 concentration with Lipid14, TIP3p and Dang or ECC ions
<p>flat POPC bilayer simulations at various NaCl and CaCl2 concentration</p> <p>modelled with Lipid14 force field, TIP3p water model and Dang or ECC ions.</p> <p>file names report molar fraction of cations (i.e. not bulk concentrations).</p> <p>simulations performed with Gromacs 5.1.4 (*.xtc files) and openMM 7 (*.dcd files)</p> <p>simulation length 300 ns</p> <p>temperature 313 K (otherwise noted)</p>
Simulations of POPC lipid bilayer in water solution with various molar fractions of cationic surfactant dihexadecylammonium using ECC-POPC force field
<p>Classical molecular dynamics simulations of a POPC lipid bilayer in water solution with various molar fractions of cationic surfactant dihexadecylammonium using ECC-POPC force field parameters, SPC/E water model and ECC-ions.</p> <p>Simulation at pure water is in a separate Zenodo deposit<br> https://doi.org/10.5281/zenodo.1118266</p> <p>file names report molar fraction of cations (i.e. not bulk concentrations)</p> <p>simulations performed with Gromacs 5.1.4 (*.xtc files) and openMM 7 (*.dcd files)</p> <p>simulation length 200 ns</p> <p>temperature 313 K (otherwise noted)</p>
Simulations of POPC lipid bilayer in water solution at various NaCl and CaCl2 concentrations using ECC-POPC force field and various water models
<p>Classical molecular dynamics simulations of a POPC lipid bilayer in water solution at various NaCl and CaCl2 concentrations using ECC-POPC force field parameters, various water models and ECC-ions.</p> <p>Simulations with SPC/E water model are in a separate Zenodo deposit<br> https://doi.org/10.5281/zenodo.1118266</p> <p>file names report molar fraction of cations (i.e. not bulk concentrations)</p> <p>simulations performed with Gromacs 5.1.4 (*.xtc files) and openMM 7 (*.dcd files)</p> <p>simulation length 300 ns</p> <p>temperature 313 K (otherwise noted)</p>
Molecular dynamics simulations of lipid bilayers containing POPC and POPS (various mixtures) with ECC-lipids force field, and Na+ (K+) counterions
<p>Classical molecular dynamics simulations of various mixtures of POPC:POPS lipid bilayers in water solution with only Na+ counterions (or with K+ counterions when noted with "_KCl" suffix).</p> <p>ECC-lipids force field parameters used for lipids, SPC/E water model and ECC-ions, all parameters available at <a href="https://github.com/jmelcr/ecc_lipids">https://github.com/jmelcr/ecc_lipids</a></p> <p>simulations performed with Gromacs 2018.0 (*.xtc files)</p> <p>simulation length 1000 ns = 1 microsecond</p> <p>temperature 298 K</p> <p>Gromacs simulation setting is in the file npt_lipid_bilayer.mdp</p>
Molecular dynamics simulations of lipid bilayers containing POPC and POPS (5:1) with ECC-lipids force field, and Na+ (K+) counterions at various CaCl2 additional concentrations
<p>Classical molecular dynamics simulations of various mixtures of POPC:POPS lipid bilayers in water solution with Na+ counterions (or with K+ counterions when noted with "_KCl" suffix) and an additional concentration of CaCl2.</p> <p>The numbers in the file names denote the number of additional Ca2+ cations.</p> <p>ECC-lipids force field parameters used for lipids, SPC/E water model and ECC-ions, all parameters available at <a href="https://github.com/jmelcr/ecc_lipids">https://github.com/jmelcr/ecc_lipids</a></p> <p>simulations performed with Gromacs 2018.0 (*.xtc files)</p> <p>simulation length 1000 ns = 1 microsecond</p> <p>temperature 298 K</p> <p>Simulations without additional salts are at a <a href="https://doi.org/10.5281/zenodo.1488094">separate deposit: 10.5281/zenodo.1488094</a>.</p>
Simulation data for ECC-CHARMM36 POPC bilayer, 100 lipids/leaflet, 940 mM NaCl, 310K, GROMACS 5.1.4
<p>Simulations of a POPC bilayer with 940 mM of NaC. </p> <p>The sixth from the set of 6 simulations.</p> <p>The goal was to study the effect of scaling the CHARMM FF on the ion binding.</p> <p>Done for the NMRlipids project, see <br> http://nmrlipids.blogspot.fi for more information.</p> <p>A POPC bilayer consisting of 200 lipids (100 per leaflet) <br> is simulated in the presence of 945 mM NaCl. The scaled ECC-Charmm36 <br> model is employed for lipids, the Charmm compatible variant <br> of the tip3p model for water, and the ECC-ions<br> for NaCl. The new extra nonbonded parameters (NB-Fix) were removed.</p> <p> </p> <p>The Charmm36 force field parameters were obtained from http://charmm-gui.org/</p> <p>Charges of head group of POPC were scaled by 0.8, sigmas were scaled by 0.89.</p> <p>In the CHARMM FF, thera are extra sigma and epsilon parameters for 1,4 interactions (these are not present in the lipid14 FF). These parameters were not scaled here.</p> <p>This is the same scaling as used for ECC-POPC</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>The files are in GROMACS format. Trajectory (.xtc) is <br> 610 ns long with data saved every 100 ps.</p> <p>the initial structure (.gro), topology (.top), index file (.ndx), <br> simulation paremeter file (.mdp), binary run input file <br> for GROMACS v. 5.1–> (.tpr) and the energy output file <br> (.edr) are provided. </p>
Simulation data for ECC-CHARMM36 POPC bilayer, 100 lipids/leaflet, 450 mM CaCl2, 310K, GROMACS 5.1.4
<p>Simulations of a POPC bilayer with 450 mM of CaCl_2. </p> <p>The fourth from the set of 6 simulations.</p> <p>The goal was to study the effect of scaling the CHARMM FF on the ion binding.</p> <p>Done for the NMRlipids project, see <br> http://nmrlipids.blogspot.fi for more information.</p> <p>A POPC bilayer consisting of 200 lipids (100 per leaflet) <br> is simulated in the presence of 450 mM CaCl_2. The scaled ECC-Charmm36 <br> model is employed for lipids, the Charmm compatible variant <br> of the tip3p model for water, and the ECC-ions<br> for CaCl_2. The new extra nonbonded parameters (NB-Fix) were removed.</p> <p> </p> <p>The Charmm36 force field parameters were obtained from http://charmm-gui.org/</p> <p>Charges of head group of POPC were scaled by 0.8, sigmas were scaled by 0.89.</p> <p>In the CHARMM FF, thera are extra sigma and epsilon parameters for 1,4 interactions (these are not present in the lipid14 FF). These parameters were not scaled here.</p> <p>This is the same scaling as used for ECC-POPC</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>The files are in GROMACS format. Trajectory (.xtc) is <br> 610 ns long with data saved every 100 ps.</p> <p>the initial structure (.gro), topology (.top), index file (.ndx), <br> simulation paremeter file (.mdp), binary run input file <br> for GROMACS v. 5.1–> (.tpr) and the energy output file <br> (.edr) are provided. </p>
Molecular dynamics simulations of lipid bilayers containing POPC and POPS (5:1) with ECC-lipids force field, and Na+ (K+) counterions at various additional concentrations of NaCl and KCl
<p>Classical molecular dynamics simulations of various mixtures of POPC:POPS lipid bilayers in water solution with Na+ counterions (or with K+ counterions when noted with "_KCl" suffix) and an additional concentration of NaCl or KCl.</p> <p>The numbers in the file names denote the number of additional cations.</p> <p>ECC-lipids force field parameters used for lipids, SPC/E water model and ECC-ions, all parameters are included in this repository in GROMACS format and are also available at <a href="https://github.com/jmelcr/ecc_lipids">https://github.com/jmelcr/ecc_lipids</a></p> <p>simulations performed with Gromacs 2018.0 (*.xtc files)</p> <p>simulation length 1000 ns = 1 microsecond</p> <p>temperature 298 K</p> <p>Simulations without additional salts are at a <a href="https://doi.org/10.5281/zenodo.1488094">separate deposit: 10.5281/zenodo.1488094</a>.</p>
Simulations of POPC lipid bilayer in water solution at various NaCl, KCl and CaCl2 concentrations using ECC-POPC force field
<p>Classical molecular dynamics simulations of a POPC lipid bilayer in water solution at various NaCl, KCl and CaCl2 concentrations using ECC-POPC force field parameters, SPC/E water model and ECC-ions.</p> <p>file names report molar fraction of cations (i.e. not bulk concentrations)</p> <p>simulations performed with Gromacs 5.1.4 (*.xtc files) and openMM 7 (*.dcd files)</p> <p>simulation length 300 ns</p> <p>temperature 313 K (otherwise noted)</p> <p>Gromacs simulation setting is in the file npt_lipid_bilayer.mdp</p>
ECC-POPC-curved-bilayer-positive
<p>A curved POPC bilayer, restrained in the *negative* regions - positively curved regions are free to move.</p>
ECC-POPC-curved-bilayer-negative
<p>A curved POPC bilayer, restrained in the *positive* regions - negatively curved regions are free to move.</p> <p>150 mmol/l CaCl2</p>
Atraumatic Restorative Treatment (ART) in Early Childhood Caries (ECC)
ClinicalTrials.gov study NCT03756025. IPD Sharing: NO. Countries: 1. Publications: 1.
Oropharyngeal Candidiasis (OPC) and S-ECC
ClinicalTrials.gov study NCT05761197. IPD Sharing: NO. Countries: 1. Publications: 28.
POPC @ 310K, varying amounts of NaCl. Slipids with ECC-scaled ions
<p>Simulations of a POPC bilayer with varying amounts of NaCl.<br> These simulations were performed as a part of the NMRlipids<br> project (http://nmrlipids.blogspot.fi). The goal was to study <br> the effect of salt on the order parameters of the lipid head <br> group and the glycerol backbone. The obtained results are <br> reported in the blog.</p> <p>A POPC bilayer consisting of 200 lipids (100 per leaflet) is <br> simulated in the presence of NaCl. Concentrations of 130, 300, <br> 500, 750, and 1000 mM are employed. The Slipids model [1–3] is <br> employed for lipids, tip3p model for water, and the recent ion <br> parameters by Kohagen et al. [4] for NaCl. </p> <p>The Slipids force field parameters were downloaded from<br> http://mmkluster.fos.su.se/slipids/</p> <p>The ion parameters are available at<br> https://bitbucket.org/hseara/ions/</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>The files are named based on the concentration of NaCl<br> and are in GROMACS format. Trajectories (.xtc) are <br> 100 ns long with data saved every 100 ps. Additionally,<br> initial structures (.gro), topology (.top), index (.ndx)<br> and binary run input files for GROMACS v. 4.6–> (.tpr)<br> are provided. The run parameter file (.mdp) is general<br> for all systems.</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>[1] Derivation and Systematic Validation of a Refined <br> All-Atom Force Field for Phosphatidylcholine Lipids<br> Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br> The Journal of Physical Chemistry B 2012 116 (10), 3164-3179<br> DOI: 10.1021/jp212503e</p> <p> </p> <p>[2] An Extension and Further Validation of an All-Atomistic <br> Force Field for Biological Membranes<br> Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br> Journal of Chemical Theory and Computation 2012 8 (8), 2938-2948<br> DOI: 10.1021/ct300342n</p> <p> </p> <p>[3] Another Piece of the Membrane Puzzle: Extending Slipids Further<br> Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br> Journal of Chemical Theory and Computation 2013 9 (1), 774-784<br> DOI: 10.1021/ct300777p</p> <p> </p> <p>[4] Accounting for Electronic Polarization Effects in Aqueous Sodium <br> Chloride via Molecular Dynamics Aided by Neutron Scattering<br> Miriam Kohagen, Philip E. Mason, and Pavel Jungwirth<br> The Journal of Physical Chemistry B Article ASAP<br> DOI: 10.1021/acs.jpcb.5b0522</p>
ECC-POPC, 28mM, 2600mM
<p>POPC mambrane with different concentrations of calcium ions simulated with ECC-POPC force-field</p>
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