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64 results for “CaCl2”
Amber Lipid17 Simulations of POPC/POPS Membranes with CaCl2
<p><strong>System: </strong>Simulations of POPC/POPS (5:1, 144 lipids in total) membranes with various CaCl2 concentrations. </p> <p><strong>Number of POPS:</strong> 24.</p> <p><strong>Number of POPC</strong> 120.</p> <p><strong>Number of waters:</strong> 5760 (excluded from uploaded trajectories)</p> <p><strong>Number of Ca+2 Ions: </strong>52 (500mm), 104 (1000mm), 208 (2000mm), 311 (3000mm), 415 (4000mm)</p> <p><strong>Lipid model:</strong> Amber Lipid 17 [IR Gould, AA Skjevik, CJ Dickson, BD Madej, RC Walker: "Lipid17: A Comprehensive AMBER Force Field for the Simulation of Zwitterionic and Anionic Lipids" in prep. (2018)].</p> <p><strong>Ion models: </strong> Li/Merz Ions [Li, P. <em>J. Chem. Theory Comput.</em> <strong>9</strong> 2733-2748 (2013)].</p> <p><strong>Water model:</strong> TIP3P [WL Jorgensen, J Chandrasekhar, JD Madura, RW Impey, ML Klein <em>J. Chem. Phys.</em> <strong>79</strong> 926 (1983)].</p> <p><strong>Simulation engine:</strong> Amber16 [DA Case et al. <em>AMBER 2017</em> UCSF (2017)].</p> <p><strong>Number of independent repeats per setup: </strong>2.<br> <strong>Trajectory lengths per repeat:</strong> 200 ns.<br> <strong>Previously equilibrated for:</strong> 300 ns.<br> <strong>Sampling rate:</strong> every 10 ps.</p> <p><strong>Time integration step:</strong> 2 fs.</p> <p><strong>Thermodynamic ensemble:</strong> NpT. <br> <strong>Temperature coupling:</strong> 'Langevin' at T = 298 K.<br> <strong>Pressure coupling: '</strong>Berendsen' [<em>J. Chem. Phys.</em> <strong>81</strong> 3684 (1984); <em>J. Chem. Phys.</em> <strong>103</strong> 10252 (1995)] with xy and z coupled separately at p = 1.0 bar with no surface tension.</p> <p><strong>Electrostatics: </strong>PME [<em>J. Chem. Phys.</em> <strong>98</strong> 10089 (1993);<em> J. Chem. Theory Comput.</em> <strong>9</strong> 3878 (2013)].<br> <strong>Van der Waals:</strong> Turned off between 1.0 nm and 1.5 nm.</p> <p><strong>Constraints: </strong>Lengths of covalent bonds involving Hydrogens in lipids using SHAKE [<em>J. Comput. Phys.</em> <strong>23</strong> 327 (1977)], in water using SETTLE [<em>J. Comput. Chem. </em><strong>13</strong> 952 (1992)].</p> <p><strong>Used in publications: </strong>OHS Ollila et al. "NMRlipids IV: Headgroup & glycerol backbone structures, and cation binding in bilayers with PS lipids" in prep (2018).</p>
Pure POPC Membrane with 650mM 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, 76 CaCl2, and 6400 SWM4 water molecules.</p> <p>The simulation have been performed using OpenMM 7.4.1</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. 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>The initial structures have been obtained from CHARMM-GUI.</p> <p> </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_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 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 concatenated and saved in xtc format with MDAnalysis.</strong></p>
Pure POPC Membrane with 350mM 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, 41 CaCl2, and 6400 SWM4 water molecules.</p> <p>wrapped.dcd has a frame saving frequency of 100 ps.</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. The first 100 ns of the Drude simulation has been discarded from this dataset.</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_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 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 concatenated and saved in xtc format with MDAnalysis.</strong></p>
Pure POPC membrane simulations with 1000 mM CaCl2 with the CHARMM-Drude force field (OpenMM)
<p>400 ns MD simulation of pure POPC membrane using Charmm-Drude polarizable force field. The system contains 128 POPC lipids, 114 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. The first 100 ns of the Drude simulation has been discarded from this dataset. Total simulation time is 500 ns, included data is 397.5 ns.</p> <p> </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 "wrapped_full.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps and there are 39750 frames.</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 4 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><strong>Centering of the trajectories has been done via below MDAnalysis script</strong></p> <p><strong> ...: u = mda.Universe('../step3_charmm2omm.psf', 'step5.dcd')<br> ...: prot = u.select_atoms("resname POPC")<br> ...: ag = u.atoms<br> ...: workflow = (transformations.unwrap(ag),<br> ...: transformations.center_in_box(prot, center='mass'),<br> ...: transformations.wrap(ag, compound='fragments'))<br> ...: u.trajectory.add_transformations(*workflow)</strong></p> <p> </p>
Extractable NH4-N and NO3-N (2 N KCl), PO4-P (0.025 N HCl) and pH (0.01 M CaCl2) were measured on soils from a transect along the Dalton road, Arctic LTER 1991.
Extractable NH4-N and NO3-N (2 N KCl), PO4-P (0.025 N HCl) and pH (0.01 M CaCl2) were measured on soils from a transect along the Dalton road. Sites are Gus Shaver flowering sites and Arctic LTER sites.
POPC_AMBER_LIPID14_CaCl2_1Mol
<p>MD simulation trajectory and related files for fully hydrated POPC bilayer with 1M CaCl2. The LIPID14 force field was used with Gromacs 5.0.3. Ions were described by AMBER99SB-ILDN force field. Conditions: T=298.15, 128 POPC molecules, 6400 tip3p waters (lipid/water 1:50), 100 Ca, 200 Cl. 200ns trajectory (preceded by 5ns NPT equillibration) (2 files of 100ns).</p>
POPC_CHARMM36_CaCl2_035Mol
<p>The starting structure was constructed using the CHARMM-GUI Membrane Builder (http://www.charmm-gui.org/) online tool.</p> <p>All runs were performed with Gromacs 5.0.4 software package and CHARMM36 additive force field parameters obtained from CHARMM-GUI input files [1]. Conditions: T=303, 128 POPC molecules, 6400 tip3p waters (lipid/water 1:50), 35 Ca, 70 Cl. 200ns trajectory (preceded by standard CHARMM-GUI NPT equilibration) (2 files of 100ns).</p> <p>This data is ran for the nmrlipids.blospot.fi project. More details from 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> <p> </p>
POPC_CHARMM36_CaCl2_067Mol
<p>The starting structure was constructed using the CHARMM-GUI Membrane Builder (http://www.charmm-gui.org/) online tool.</p> <p>All runs were performed with Gromacs 5.0.4 software package and CHARMM36 additive force field parameters obtained from CHARMM-GUI input files [1]. Conditions: T=303, 128 POPC molecules, 6400 tip3p waters (lipid/water 1:50), 67 Ca, 134 Cl. 200ns trajectory (preceded by standard CHARMM-GUI NPT equilibration) (2 files of 100ns).</p> <p>This data is ran for the nmrlipids.blospot.fi project. More details from 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> <p> </p>
POPC_CHARMM36_CaCl2_1Mol
<p>The starting structure was constructed using the CHARMM-GUI Membrane Builder (http://www.charmm-gui.org/) online tool.</p> <p>All runs were performed with Gromacs 5.0.4 software package and CHARMM36 additive force field parameters obtained from CHARMM-GUI input files [1]. Conditions: T=303, 128 POPC molecules, 6400 tip3p waters (lipid/water 1:50), 100 Ca, 200 Cl. 200ns trajectory (preceded by standard CHARMM-GUI NPT equilibration) (2 files of 100ns).</p> <p>This data is ran for the nmrlipids.blospot.fi project. More details from 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> <p> </p>
POPC_AMBER_LIPID14_CaCl2_035Mol
<p>MD simulation trajectory and related files for fully hydrated POPC bilayer with 0.35M CaCl2. The LIPID14 force field was used with Gromacs 5.0.3. Ions were described by AMBER99SB-ILDN force field. Conditions: T=298.15, 128 POPC molecules, 6400 tip3p waters (lipid/water 1:50), 35 Ca, 70 Cl. 200ns trajectory (preceded by 5ns NPT equillibration) (2 files of 100ns).</p> <p>THE TRAJECTORY "035M_CaCl2_POPC_AMB_100_200ns.xtc" IS CORRUPTED. FOR THE UNCORRUPTED FILE PLEASE FOLLOW THE LINK: https://zenodo.org/record/46234</p> <p>This data is ran for the nmrlipids.blospot.fi project. More details from nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi</p>
MD simulation trajectory of a POPC/POPS (4:1) bilayer with 715mM CaCl2, Berger force field for lipids, scaled charges for Ca2+ and Cl-
<p>MD simulation trajectory of a POPC/POPS (4:1) bilayer with 715 mM CaCl2 (104 POPC, 24 POPS, 26 POPS, 4306 WAT, 72 Ca2+, 112 Cl-). Additional Ca2+ cations added to neutralize the negative charge of POPS (leading to total Ca2+ concentration of 919 mM). Berger force field for lipids, scaled charges employed for calcium and chloride ions. Gromacs 4.5.5, T=310K, 300 ns trajectories were calculated with the last 100 ns stored here.</p> <p>Used in (see therein also a detailed description of ion scaling):</p> <p>A. Melcrova, S. Pokorna, S. Pullanchery, M. Kohagen, P. Jurkiewicz, M. Hof, P. Jungwirth, P. S. Cremer, L. Cwiklik, The complex nature of calcium cation interactions with phospholipid bilayers<br> Scientific Reports 2016, 6, 38035.<br> DOI: 10.1038/srep38035</p>
MD simulation trajectory of a POPC bilayer with 716mM CaCl2, Berger force field for lipids, scaled charges for Ca2+ and Cl-
<p>MD simulation trajectory of a POPC bilayer with 716 mM CaCl2 (128 POPC, 26 POPS, 4308 WAT, 56 Ca2+, 112 Cl-). Berger force field for lipids, scaled charges employed for calcium and chloride ions. Gromacs 4.5.5, T=310K, 200 ns trajectories were calculated with the last 100 ns stored here.</p> <p>Used in (see therein also a detailed description of ion scaling):</p> <p>A. Melcrova, S. Pokorna, S. Pullanchery, M. Kohagen, P. Jurkiewicz, M. Hof, P. Jungwirth, P. S. Cremer, L. Cwiklik, The complex nature of calcium cation interactions with phospholipid bilayers<br> Scientific Reports 2016, 6, 38035.<br> DOI: 10.1038/srep38035</p>
MD simulation trajectory of a POPC/POPS (4:1) bilayer with 102mM CaCl2, Berger force field for lipids, scaled charges for Ca2+ and Cl-
<p>MD simulation trajectory of a POPC/POPS (4:1) bilayer with 102 mM CaCl2 (104 POPC, 24 POPS, 26 POPS, 4306 WAT, 24 Ca2+, 16 Cl-). Additional Ca2+ cations added to neutralize the negative charge of POPS (leading to total Ca2+ concentration of 306 mM). Berger force field for lipids, scaled charges employed for calcium and chloride ions. Gromacs 4.5.5, T=310K, 300 ns trajectories were calculated with the last 100 ns stored here.</p> <p>Used in (see therein also a detailed description of ion scaling):</p> <p>A. Melcrova, S. Pokorna, S. Pullanchery, M. Kohagen, P. Jurkiewicz, M. Hof, P. Jungwirth, P. S. Cremer, L. Cwiklik, The complex nature of calcium cation interactions with phospholipid bilayers<br> Scientific Reports 2016, 6, 38035.<br> DOI: 10.1038/srep38035</p>
MD simulation trajectory of a POPC bilayer with 100mM CaCl2, Berger force field for lipids, scaled charges for Ca2+ and Cl-
<p>MD simulation trajectory of a POPC bilayer with 100 mM CaCl2 (128 POPC, 26 POPS, 4452 WAT, 8 Ca2+, 16 Cl-). Berger force field for lipids, scaled charges employed for calcium and chloride ions. Gromacs 4.5.5, T=310K, 200 ns trajectories were calculated with the last 100 ns stored here).</p> <p>Used in (see therein also a detailed description of ion scaling):</p> <p>A. Melcrova, S. Pokorna, S. Pullanchery, M. Kohagen, P. Jurkiewicz, M. Hof, P. Jungwirth, P. S. Cremer, L. Cwiklik, The complex nature of calcium cation interactions with phospholipid bilayers<br> Scientific Reports 2016, 6, 38035.<br> DOI: 10.1038/srep38035</p>
Research data for the paper: Adsorption Desalination and Cation Exchange of NaCl and CaCl2-water solutions in LTA zeolites
<p>Adsorption isotherms data of water in LTA zeolites (LTA_Si, NaLTA, CaLTA and NaCaLTA) with 0 Salt, 7 molecs/uc NaCl, 21 molecs/uc NaCl, 7 molecs/uc CaCl2, 21 molecs/uc CaCl2.</p> <p>Water adsorption data in MFI zeolite for force field validation</p> <p>Raw data of Radial Distribution Functions (RDFs) in NaLTA (LTA4A), NaCaLTA (LTA5A), CaLTA (LTACa), distances between structure (Oa), extra framework cations (NaCAT, CaCAT), salt cation (Na, Ca), and water (Ospce)</p> <p> </p>
POPC_AMBER_LIPID14_CaCl2_035Mol
<p>THIS IS UNCORRUPTED TRAJECTORY RELATED TO THIS DATASET: http://dx.doi.org/10.5281/zenodo.34415</p> <p> </p> <p>MD simulation trajectory and related files for fully hydrated POPC bilayer with 0.35M CaCl2. The LIPID14 force field was used with Gromacs 5.0.3. Ions were described by AMBER99SB-ILDN force field. Conditions: T=298.15, 128 POPC molecules, 6400 tip3p waters (lipid/water 1:50), 35 Ca, 70 Cl. 200ns trajectory (preceded by 5ns NPT equillibration) (2 files of 100ns).</p> <p> </p> <p> </p> <p>This data is ran for the nmrlipids.blospot.fi project. More details from nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi</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>
LIPID17 POPC-POPG 80:20 MD simulation, Na+ counterions and 100mM CaCl2, 298K
<p>The last 250ns of a 400ns MD simulation trajectory with Amber lipid 17 force field. POPC-POPG 80:20, (350 POPC, 88 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 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>
ECC-LIPID17 POPC-POPG 50:50 MD simulation, Na+ counterions and 100mM CaCl2, 298K
<p>Simulation data and parameters of ECC-LIPID17 simulation of POPC:POPG 50:50 mixture with Na+ counterions and 100mM CaCl2 at 298K, ran for NMRlipidsIVb:</p> <p>https://github.com/NMRLipids/NMRlipidsIVPEandPG/blob/master/Manuscript/manuscriptPGPE.pdf</p> <p>ECC-ion parameters are from bitbucket.org/hseara/ions/src/master/</p>
ECC-LIPID17 POPC-POPG 50:50 MD simulation, Na+ counterions and 1000mM CaCl2, 298K
<p>Simulation data and parameters of ECC-LIPID17 simulation of POPC:POPG 50:50 mixture with Na+ counterions and 1000mM CaCl2 at 298K, ran for NMRlipidsIVb:</p> <p>https://github.com/NMRLipids/NMRlipidsIVPEandPG/blob/master/Manuscript/manuscriptPGPE.pdf</p> <p>ECC-ion parameters are from bitbucket.org/hseara/ions/src/master/</p>
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