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306 results for “POPC”
Dataset of "Molecular Dynamics Simulations Unveil the Aggregation Patterns and Salting out of Polyarginines at Zwitterionic POPC Bilayers in Solutions of Various Ionic Strengths"
<p>Molecular dynamics simulations are performed for a series of model cell-penetrating peptides (in particular nona-arginines) in aqueous solutions, in contact with model phosphocholine (POPC) membranes in conditions of different ionic strengths. The unusual aggregation properties of peptides at model lipid bilayers are analyzed and different sizes and lifetimes of aggregates are presented.<br>This dataset contains molecular dynamics simulation data with trajectories, input files, and topology files for all studied systems. They contain low peptide concentration in water, low NaCl concentration, high NaCl concentration, low CaCl2 concentration, and high CaCl2 concentration.<br>In addition to low peptide concentration, high peptide concentration in water, low NaCl concentration, high NaCl concentration, low CaCl2 concentration, and high CaCl2 concentration are also studied.</p>
Pure POPC Membrane Simulation Using Charmm-Drude Force Field with OpenMM
<p>400 ns MD simulation of pure POPC membrane using Charmm-Drude polarizable force field. The system contains 72 POPC lipids and 2809 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>This dataset does not contain the water molecules.</p> <p><strong>Please note that</strong> the trajectories might need to be realigned.</p>
Simulation files for POPC lipid membrane with Slipids-VIS force field for Gromacs MD simulation engine
<p>The tar.gz archive contains simulation input files that were used in the publication Transmembrane potential modeling: Comparison between methods of constant electric field and ion imbalance.</p> <p>http://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b01202</p> <p>The files are meant to be used with <strong>Gromacs</strong> simulation package (gromacs.org).</p> <p>A modified Slipids force field, <strong>Slipids-VIS</strong>, is introduced. It uses Virtual Interaction sites in order to speed up simulation. The technique is described in the aforementioned work. The archive contains working topology for <strong>POPC</strong> lipid molecules and 6fs timestep without any significant loss of accuracy.</p>
Gaussian-accelerated Molecular Dynamics simulations of CCR8-CCL1-Gprotein complex in a POPC lipid bilayer
<p>Gaussian-accelerated Molecular Dynamics simulations of the CCR8-CCL1-Gprotein complex in a POPC lipid bilayer. Simulation system was prepared with OpenMM v7.7 and simulations were performed using the GaMD-OpenMM package (https://github.com/MiaoLab20/gamd-openmm) with a modification to include the MDTraj h5 file formate reporter as the output file format. These simulations were then converted to pdb topologies and dcd trajectories using MDTraj. </p><p>Files include:</p><p>CCL1_CCR8_noSer23_oriented_repaired1_system.pdb : system topology</p><p>CCL1_CCR8_config.xml : config for running GaMD-OpenMM</p><p>CCL1_CCR8_N_1ns_imaged_structure.pdb : initial topology/structure</p><p>CCL1_CCR8_N_1ns_imaged_trajectory.dcd : trajectory file</p><p> </p><p>Simulations can be loaded in python using MDTraj:</p><p>import mdtraj</p><p>trj = mdtraj.load(<dcd file>, top=<pdb file>)</p>
Simulations POPC bilayers (512 lipids) using charmm36 ff in gromacs
<p>Collection simulations of POPC (512 lipids) bilayers in gromacs using the charmm36 force field. The list of systems can be found below where the several parameter are:</p> <ol> <li>POPC_512_310K (500ns)</li> <li>POPC_512_NaCl_150mM_310K (500ns)</li> <li>POPC_512_NaCl_150mM_310K_tip3p (500ns)</li> <li>POPC_512_NaCl_Dang_150mM_310K (500ns)</li> </ol> <p>For further information read the Readme file provided for each simulation.</p>
Simulation POPC_512_TM3_10_5up_5down_NaCl_150mM_310K (rep4)
<p><strong>Title publication: </strong><em>A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction</em></p> <p><strong>Year publication: </strong>2018</p> <p><strong>DOI publication: </strong>10.1021/acscentsci.7b00582</p> <p><strong>Description:</strong> Simulation POPC membrane containing ten LAPTM4B-TM3 peptides using charmm36 at 310K.</p> <p><strong>MD engine:</strong> 2016.1<br> <br> </p> <p><strong>Force field</strong>: charmm36</p> <p><strong>Temperature</strong>: 310 K</p> <p><strong>Pressure:</strong> 1 bar</p> <p><strong>Simulation time</strong>: 2184 ns</p> <p><strong>Saving frequency</strong>: 100 ps</p> <p><strong>Molecular content</strong>:</p> <p>TM3 10<br> POPC 512<br> SOL 29366<br> NA 89<br> CL 79</p> <p><strong>Additional </strong><strong>information</strong>:<br> * Membrane containing LAPTM4B TM3 peptides.</p>
Simulation POPC_512_TM3_10_5up_5down_NaCl_150mM_310K (rep2)
<p><strong>Title publication:</strong> <em>A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction</em></p> <p><strong><strong>Year publication:</strong></strong><strong> </strong>2018</p> <p><strong>DOI publication: </strong>10.1021/acscentsci.7b00582</p> <p><strong>Description:</strong> Simulation POPC membrane containing ten LAPTM4B-TM3 peptides using charmm36 at 310K.</p> <p><strong>MD engine:</strong> 2016.1</p> <p><strong>Force field</strong>: charmm36</p> <p><strong>Temperature</strong>: 310 K</p> <p><strong>Pressure:</strong> 1 bar</p> <p><strong>Simulation time</strong>: 2080 ns</p> <p><strong>Saving frequency</strong>: 100 ps</p> <p><strong>Molecular content</strong>:</p> <p>TM3 10<br> POPC 512<br> SOL 29366<br> NA 89<br> CL 79</p> <p><strong>Additional </strong><strong>information</strong>:<br> * Membrane containing LAPTM4B TM3 peptides.</p>
Simulation POPC_512_TM3_10_5up_5down_NaCl_150mM_310K (rep3)
<p><strong>Title publication: </strong><em>A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction</em></p> <p><strong><strong>Year publication:</strong></strong><strong> </strong>2018</p> <p><strong>DOI publication: </strong>10.1021/acscentsci.7b00582</p> <p><strong>Description:</strong> Simulation POPC membrane containing ten LAPTM4B-TM3 peptides using charmm36 at 310K.</p> <p><strong>MD engine:</strong> 5.1.3-dev-20160627-f16daab<br> <br> </p> <p><strong>Force field</strong>: charmm36</p> <p><strong>Temperature</strong>: 310 K</p> <p><strong>Pressure:</strong> 1 bar</p> <p><strong>Simulation time</strong>: 2068 ns</p> <p><strong>Saving frequency</strong>: 100 ps</p> <p><strong>Molecular content</strong>:</p> <p>TM3 10<br> POPC 512<br> SOL 29366<br> NA 89<br> CL 79</p> <p><strong>Additional </strong><strong>information</strong>:<br> * Membrane containing LAPTM4B TM3 peptides.</p>
Simulation POPC_512_TM3_10_5up_5down_NaCl_150mM_310K (rep1)
<p><strong>Title publication: </strong><em>A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction</em></p> <p><strong><strong>Year publication:</strong></strong><strong> </strong>2018</p> <p><strong>DOI publication:</strong> 10.1021/acscentsci.7b00582</p> <p><strong>Description:</strong> Simulation POPC membrane containing ten LAPTM4B-TM3 peptides using charmm36 at 310K.</p> <p><strong>MD engine:</strong> 2016.1</p> <p><strong>Force field</strong>: charmm36</p> <p><strong>Temperature</strong>: 310 K</p> <p><strong>Pressure:</strong> 1 bar</p> <p><strong>Simulation time</strong>: 2018 ns</p> <p><strong>Saving frequency</strong>: 100 ps</p> <p><strong>Molecular content</strong>:</p> <p>TM3 10<br> POPC 512<br> SOL 29366<br> NA 89<br> CL 79</p> <p><strong>Additional </strong><strong>information</strong>:<br> * Membrane containing LAPTM4B TM3 peptides.</p>
Simulation CER160_9_POPC_512_TM3_10_5up_5down_NaCl_150mM_310K (rep6)
<p><strong>Title publication: </strong><em>A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction</em></p> <p><strong><strong>Year publication:</strong></strong> 2018</p> <p><strong>DOI publication: </strong>10.1021/acscentsci.7b00582</p> <p><strong>Description:</strong> Simulation POPC membrane containing ten LAPTM4B-TM3 peptides and 9 ceramide (CER160) originally in the water phase using charmm36 at 310K.</p> <p><strong>MD engine:</strong> 2018</p> <p><strong>Force field</strong>: charmm36</p> <p><strong>Temperature</strong>: 310 K</p> <p><strong>Pressure:</strong> 1 bar</p> <p><strong>Simulation time</strong>: 609 ns</p> <p><strong>Saving frequency</strong>: 100 ps</p> <p><strong>Molecular content</strong>:</p> <p>TM3 10<br> POPC 512<br> CER160 9<br> SOL 34248<br> NA 102<br> CL 92</p> <p><strong>Additional </strong><strong>information</strong>:<br> * Membrane containing LAPTM4B TM3 peptides.</p>
Simulation CER160_9_POPC_512_TM3_10_5up_5down_NaCl_150mM_310K (rep1)
<p><strong>Title publication:</strong> <em>A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction</em></p> <p><strong>Year publication:</strong> 2018</p> <p><strong>DOI publication: </strong>10.1021/acscentsci.7b00582</p> <p><strong>Description:</strong> Simulation POPC membrane containing ten LAPTM4B-TM3 peptides and 9 ceramide (CER160) originally in the water phase using charmm36 at 310K.</p> <p><strong>MD engine:</strong> 2016.2-dev-20170105-4feb0be</p> <p><strong>Force field</strong>: charmm36</p> <p><strong>Temperature</strong>: 310 K</p> <p><strong>Pressure:</strong> 1 bar</p> <p><strong>Simulation time</strong>: 2134 ns</p> <p><strong>Saving frequency</strong>: 100 ps</p> <p><strong>Molecular content</strong>:</p> <p>TM3 10<br> POPC 512<br> CER160 9<br> SOL 34248<br> NA 102<br> CL 92</p> <p><strong>Additional </strong><strong>information</strong>:<br> * Membrane containing LAPTM4B TM3 peptides.</p>
Simulation CER160_9_POPC_512_TM3_10_5up_5down_NaCl_150mM_310K (rep4)
<p><strong>Title publication: </strong><em>A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction</em></p> <p><strong><strong>Year publication:</strong></strong><strong> </strong>2018</p> <p><strong>DOI publication: </strong>10.1021/acscentsci.7b00582</p> <p><strong>Description:</strong> Simulation POPC membrane containing ten LAPTM4B-TM3 peptides and 9 ceramide (CER160) originally in the water phase using charmm36 at 310K.</p> <p><strong>MD engine:</strong> 2018</p> <p><strong>Force field</strong>: charmm36</p> <p><strong>Temperature</strong>: 310 K</p> <p><strong>Pressure:</strong> 1 bar</p> <p><strong>Simulation time</strong>: 648 ns</p> <p><strong>Saving frequency</strong>: 100 ps</p> <p><strong>Molecular content</strong>:</p> <p>TM3 10<br> POPC 512<br> CER160 9<br> SOL 34248<br> NA 102<br> CL 92</p> <p><strong>Additional </strong><strong>information</strong>:<br> * Membrane containing LAPTM4B TM3 peptides.</p>
Simulation CER160_9_POPC_512_NaCl_150mM_310K (rep1)
<p><strong>Title publication: </strong><strong><em>A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction</em></strong></p> <p><strong><strong>Year publication:</strong></strong><strong> 2018</strong></p> <p><strong>DOI publication: </strong><strong>10.1021/acscentsci.7b00582</strong></p> <p><strong>Description:</strong> Simulation POPC membrane containing 9 ceramide (CER160) originally in the water phase using charmm36 at 310K.</p> <p><strong>MD engine:</strong> 2016.5</p> <p><strong>Force field</strong>: charmm36</p> <p><strong>Temperature</strong>: 310 K</p> <p><strong>Pressure:</strong> 1 bar</p> <p><strong>Simulation time</strong>: 3038 ns</p> <p><strong>Saving frequency</strong>: 100 ps</p> <p><strong>Molecular content</strong>:<br> POPC 512<br> CER160 9<br> SOL 34258<br> NA 92<br> CL 92</p>
Simulation CER160_9_POPC_512_TM3_10_5up_5down_NaCl_150mM_310K (rep3)
<p><strong>Title publication:</strong> <em>A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction</em></p> <p><strong><strong>Year publication:</strong></strong><strong> </strong>2018</p> <p><strong>DOI publication: </strong>10.1021/acscentsci.7b00582</p> <p><strong>Description:</strong> Simulation POPC membrane containing ten LAPTM4B-TM3 peptides and 9 ceramide (CER160) originally in the water phase using charmm36 at 310K.</p> <p><strong>MD engine:</strong> 2016.2-dev-20170105-4feb0be</p> <p><strong>Force field</strong>: charmm36</p> <p><strong>Temperature</strong>: 310 K</p> <p><strong>Pressure:</strong> 1 bar</p> <p><strong>Simulation time</strong>: 1980 ns</p> <p><strong>Saving frequency</strong>: 100 ps</p> <p><strong>Molecular content</strong>:</p> <p>TM3 10<br> POPC 512<br> CER160 9<br> SOL 34248<br> NA 102<br> CL 92</p> <p><strong>Additional </strong><strong>information</strong>:<br> * Membrane containing LAPTM4B TM3 peptides.</p>
Simulation CER160_9_POPC_512_TM3_10_5up_5down_NaCl_150mM_310K (rep2)
<p><strong>Title publication:</strong> <em>A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction</em></p> <p><strong><strong>Year publication:</strong></strong> 2018</p> <p><strong>DOI publication: </strong>10.1021/acscentsci.7b00582</p> <p><strong>Description:</strong> Simulation POPC membrane containing ten LAPTM4B-TM3 peptides and 9 ceramide (CER160) originally in the water phase using charmm36 at 310K.</p> <p><strong>MD engine:</strong> 2016.2-dev-20170105-4feb0be</p> <p><strong>Force field</strong>: charmm36</p> <p><strong>Temperature</strong>: 310 K</p> <p><strong>Pressure:</strong> 1 bar</p> <p><strong>Simulation time</strong>: 4583 ns</p> <p><strong>Saving frequency</strong>: 100 ps</p> <p><strong>Molecular content</strong>:</p> <p>TM3 10<br> POPC 512<br> CER160 9<br> SOL 34248<br> NA 102<br> CL 92</p> <p><strong>Additional </strong><strong>information</strong>:<br> * Membrane containing LAPTM4B TM3 peptides.</p>
Simulation CER160_9_POPC_512_TM3_10_5up_5down_NaCl_150mM_310K (rep5)
<p><strong>Title publication:</strong> <em>A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction</em></p> <p><strong><strong>Year publication:</strong></strong><strong> </strong>2018</p> <p><strong>DOI publication: </strong>10.1021/acscentsci.7b00582</p> <p><strong>Description:</strong> Simulation POPC membrane containing ten LAPTM4B-TM3 peptides and 9 ceramide (CER160) originally in the water phase using charmm36 at 310K.</p> <p><strong>MD engine:</strong> 2018</p> <p><strong>Force field</strong>: charmm36</p> <p><strong>Temperature</strong>: 310 K</p> <p><strong>Pressure:</strong> 1 bar</p> <p><strong>Simulation time</strong>: 318 ns</p> <p><strong>Saving frequency</strong>: 100 ps</p> <p><strong>Molecular content</strong>:</p> <p>TM3 10<br> POPC 512<br> CER160 9<br> SOL 34248<br> NA 102<br> CL 92</p> <p><strong>Additional </strong><strong>information</strong>:<br> * Membrane containing LAPTM4B TM3 peptides.</p>
Simulation CER160_9_POPC_512_NaCl_150mM_310K (rep2)
<p><strong>Title publication: </strong><em>A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction</em></p> <p><strong><strong>Year publication:</strong></strong><strong> </strong>2018</p> <p><strong>DOI publication:</strong> 10.1021/acscentsci.7b00582</p> <p><strong>Description:</strong> Simulation POPC membrane containing 9 ceramide (CER160) originally in the water phase using charmm36 at 310K.</p> <p><strong>MD engine:</strong> 2016.5</p> <p><strong>Force field</strong>: charmm36</p> <p><strong>Temperature</strong>: 310 K</p> <p><strong>Pressure:</strong> 1 bar</p> <p><strong>Simulation time</strong>: 3038 ns</p> <p><strong>Saving frequency</strong>: 100 ps</p> <p><strong>Molecular content</strong>:<br> POPC 512<br> CER160 9<br> SOL 34258<br> NA 92<br> CL 92</p>
Pure POPC Membrane with 1000mM NaCl 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, 115 NaCl, 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><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 450mM NaCl 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, 51 NaCl, 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><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 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>
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