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Dataset results
119 results for “gromacs”
MD simulation trajectory and related files for POPC bilayer with 340mM CaCl_2 (Berger model delivered by Tieleman, ffgmx ions, Gromacs 4.5)
<p>Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, Berger force field delivered by Peter Tieleman (http://wcm.ucalgary.ca/tieleman/downloads) double bonds updated in http://dx.doi.org/10.1021/jp065424f, ffgmx parameters for ions, 50ns, T=298K, 128 POPC molecules, 7157 water molecules, 44 Na molecules, 88 Cl molecules. This data is used in the NMRLipids II project (nmrlipids.blospot.fi).</p>
MD simulation trajectory and related files for POPC bilayer with 950mM NaCl (CHARMM36, Gromacs 4.5)
<p>Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, CHARMM36, 60ns, T=303K, 72 POPC molecules, 2085 water molecules, 37 Na molecules, 37 Cl molecules. This data is used in the NMRLipids II project (nmrlipids.blospot.fi).</p>
MD simulation trajectory and related files for POPC bilayer with 690mM NaCl (CHARMM36, Gromacs 4.5)
<p>Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, CHARMM36, 60ns, T=303K, 72 POPC molecules, 2085 water molecules, 26 Na molecules, 26 Cl molecules. This data is used in the NMRLipids II project (nmrlipids.blospot.fi).</p>
MD simulation trajectory for POPC bilayer (Orange, Gromacs 4.5.)
<p>Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, Orange, 50ns, T=298K, 72 POPC molecules, 2880 water molecules. This data is used in the NMRLipids II project (nmrlipids.blospot.fi, https://github.com/NMRLipids/lipid_ionINTERACTION).</p> <p> </p> <p>The Orange model is unpublished lipid model developed by Luca Monticelli et al. http://perso.ibcp.fr/luca.monticelli/research/index.html. Beta version of the model is used here, thus only trajectory is shared.</p> <p> </p>
MD simulation trajectory for POPC bilayer with 510mM CaCl_2 (Orange, Gromacs 4.5.)
<p>Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, Orange, 60ns, T=298K, 72 POPC molecules, 2802 water molecules, 26 Ca molecules, 52 Cl molecules. This data is used in the NMRLipids II project (nmrlipids.blospot.fi, https://github.com/NMRLipids/lipid_ionINTERACTION).</p> <p> </p> <p>The Orange model is unpublished lipid model developed by Luca Monticelli et al. http://perso.ibcp.fr/luca.monticelli/research/index.html. Beta version of the model is used here, thus only trajectory is shared.</p>
MD simulation trajectory and related files for POPC bilayer with 30 mol% of deprotonated pazePC (Berger, Gromacs 4.5.)
<p>Simulation trajectory and related files for POPC bilayer with 30mol% of pazePC in deprotonated form used in "Acyl chain disorder and azelaoyl orientation in lipid membranes containing oxidised lipids" by T. M. Ferreira, et al., https://doi.org/10.1021/acs.langmuir.6b00788.</p> <p> </p> <p>90 POPC, 38 pazePC, 7250 water and 38 potassium molecules. Simulation time 120ns.</p> <p> </p> <p>Force field for POPC is based on Berger model and force field for pazePC is from H. Khandelia and O. G. Mouritsen, Biophysical Journal, 2009, 96(7), 2734 – 2743, http://dx.doi.org/10.1016/j.bpj.2009.01.007.</p> <p> </p> <p>If used, please cite approriate publications.</p>
MD simulation trajectory and related files for POPC bilayer with 30 mol% of protonated pazePC (Berger, Gromacs 4.5.)
<p>Simulation trajectory and related files for POPC bilayer with 30mol% of pazePC in deprotonated form used in "Acyl chain disorder and azelaoyl orientation in lipid membranes containing oxidised lipids" by T. M. Ferreira, et al. https://doi.org/10.1021/acs.langmuir.6b00788</p> <p><br> The simulation with deprotonated pazePC from the same publication available at http://dx.doi.org/10.5281/zenodo.44622</p> <p>90 POPC, 38 pazePC, 7250 water and 38 potassium molecules. Simulation time 167ns.</p> <p> </p> <p>Force field for POPC is based on Berger model and force field for pazePC is modified from H. Khandelia and O. G. Mouritsen, Biophysical Journal, 2009, 96(7), 2734 – 2743, http://dx.doi.org/10.1016/j.bpj.2009.01.007.</p>
MD simulation trajectory for POPC bilayer with 140mM NaCl (Orange, Gromacs 4.5.)
<p>Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, Orange, 60ns, T=298K, 72 POPC molecules, 2866 water molecules, 7 Na molecules, 7 Cl molecules. This data is used in the NMRLipids II project (nmrlipids.blospot.fi, https://github.com/NMRLipids/lipid_ionINTERACTION).</p> <p> </p> <p>The Orange model is unpublished lipid model developed by Luca Monticelli et al. http://perso.ibcp.fr/luca.monticelli/research/index.html. Beta version of the model is used here, thus only trajectory is shared.</p>
MD simulation trajectory for POPC bilayer with 510mM NaCl (Orange, Gromacs 4.5.)
<p>Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, Orange, 120ns, T=298K, 72 POPC molecules, 2802 water molecules, 26 Na molecules, 26 Cl molecules. This data is used in the NMRLipids II project (nmrlipids.blospot.fi, https://github.com/NMRLipids/lipid_ionINTERACTION).</p> <p> </p> <p>The Orange model is unpublished lipid model developed by Luca Monticelli et al. http://perso.ibcp.fr/luca.monticelli/research/index.html. Beta version of the model is used here, thus only trajectory is shared.</p>
MD simulation trajectory for POPC bilayer with 1000mM NaCl (Orange, Gromacs 4.5.)
<p>Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, Orange, 120ns, T=298K, 72 POPC molecules, 2780 water molecules, 50 Na molecules, 50 Cl molecules. This data is used in the NMRLipids II project (nmrlipids.blospot.fi, https://github.com/NMRLipids/lipid_ionINTERACTION).</p> <p> </p> <p>The Orange model is unpublished lipid model developed by Luca Monticelli et al. http://perso.ibcp.fr/luca.monticelli/research/index.html. Beta version of the model is used here, thus only trajectory is shared.</p>
MD simulation trajectory and related files for POPC bilayer with 670mM CaCl_2 (CHARMM36, Gromacs 4.5)
<p>Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, CHARMM36, 120ns, T=303K, 72 POPC molecules, 2165 water molecules, 26 Ca molecules, 52 Cl molecules.</p> <p>Note! This dataset is NOT used in the NMRLipids II project (nmrlipids.blospot.fi), but the dataset http://dx.doi.org/10.5281/zenodo.35160</p> <p>See also discussion in: https://github.com/NMRLipids/lipid_ionINTERACTION/issues/16</p>
SDS micelle, MD simulation, Gromacs 5.0, CHARMM36
<p>Molecular dynamics simulation of SDS micelle. Gromacs 5.0, CHARMM36. Files generated with CHARMM GUI. System contains 60 SDS molecules, 16854 water molecules and 60 sodium ions. Temperature T=293K. Length is 20ns.</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>
CHARMM36 POPC GROMACS 5.0.6 500 ns (started from TJP files)
<p>CHARMM36 force field POPC simulations performed using GROMACS version 5.0.6 started from structure and POPC topology obtained from http://pubs.acs.org/doi/abs/10.1021/ct3003157 and the CHARMM36 force field parameters from http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs. Results are included for simulations using both an 8 Å and 10 Å switching point for the van der Waals interactions, with 2 x 500 ns for each of these cut-off schemes (versions with different starting velocities are labelled as v1 and v2). The trajectories have been processed using trjconv -skip 10 to make the files smaller for uploading, although the initial analysis was performed on the complete simulations.</p>
CHARMM36 POPC GROMACS 5.0.6 500 ns (started from JM files)
<p>CHARMM36 force field POPC simulations performed using GROMACS version 5.0.6 started from files obtained from https://doi.org/10.5281/zenodo.153944. Results are included for simulations using both an 8 Å and 10 Å switching point for the van der Waals interactions, with 4 x 500 ns for each of these cut-off schemes (versions with different starting velocities are labelled as v1, v2, v3 and v4). The trajectories have been processed using trjconv -skip 10 to make the files smaller for uploading, although the initial analysis was performed on the complete simulations.</p>
GROMACS Coordinates and force field files for the SC lipid barrier
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Amyloid-beta 16-22 peptide dimer simulation (150mM NaCl) with the CHARMM36m force field and Gromacs (Run 2)
<p>Amyloid-beta 16-22 peptide dimer simulation with the CHARMM36m force field. This directory contains the second of the three independent trajectories and the simulation length is 1 microseconds. The system contains two amyloid-beta 16-22 monomers, 30 Na+, 30 Cl-, and 10564 TIP3P water.</p>
Amyloid-beta 16-22 peptide dimer simulation (150mM NaCl) with the CHARMM36m force field and Gromacs (Run 1)
<p>Amyloid-beta 16-22 peptide dimer simulation with the CHARMM36m force field. This directory contains first of the three independent trajectories and the simulation length is 1 microseconds. The system contains two amyloid-beta 16-22 monomers, 30 Na+, 30 Cl-, and 10564 TIP3P water.</p>
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International Brain Laboratory public data
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OpenNeuro
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