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158 results for “Charmm36”
POPC/Cholesterol (70:30) lipid membrane, 303K, Charmm36 force field through the use of Gromacs input files, simulation files and 100 ns trajectory for openMM simulation engine v7
<p>The starting structure was obtained from CHARMM-GUI Membrane Builder v1.7 (http://www.charmm-gui.org/) online tool. [1]</p> <p>All runs were performed with openMM simulation engine v7 and CHARMM36 additive force field parameters obtained from CHARMM-GUI input files [1]. Specifically, Gromacs file format provided by [1] was specifically used for this simulation.</p> <p>Conditions: T=303, 84 POPC and 36 Cholesterol molecules, 4800 tip3p waters, 100ns trajectory (preceded with equilibration).</p> <p>These data were originally obtained for the nmrlipids.blospot.fi project.</p> <p>Find more details at 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>
POPC/Cholesterol (50:50) lipid membrane, 303K, Charmm36 force field, simulation files and 100 ns trajectory for GROMACS simulation engine v5
<p>All runs were performed with GROMACS simulation engine v5 and CHARMM36 additive force field parameters obtained from MacKerell lab website (http://mackerell.umaryland.edu/charmm_ff.shtml, also available at</p> <p>https://doi.org/10.5281/zenodo.209080). Conditions: T=303, 80 POPC and 80 Cholesterol molecules, 7200 tip3p waters, 100ns trajectory (preceded with equilibration). </p> <p>These data were originally obtained for the nmrlipids.blospot.fi project.</p> <p>Find more details at nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi</p>
Re-charging your fats: Charmm36 parameters for neutral lipids triacylglycerol and diacylglycerol
<p>Dataset containing files required to run the simulations and reproduce the Figures appearing in "Re-charging your fats: Charmm36 parameters for neutral lipids triacylglycerol and diacylglycerol"</p>
Simulations DSPC bilayers (512 lipids) using charmm36 ff in gromacs
<p>Collection simulations of DSPC (512 lipids) bilayers in gromacs using the charmm36 force field. Temperatures of 333 and 338 K are included. The list of systems can be found below:</p> <p>1) DSPC_512_NaCl_150mM_333K (620ns)<br> 2) DSPC_512_NaCl_150mM_338K (500ns)</p> <p>For further information read the Readme file provided for each simulation.</p>
Simulations DPPC bilayers (512 lipids) using charmm36 ff in gromacs
<p>Collection simulations of DPPC (512 lipids) bilayers in gromacs using the charmm36 force field. Several temperatures between 315 and 338 K are included. The list of systems can be found below where the several parameter are:</p> <p>1) DPPC_512_NaCl_150mM_315K_v-rescale (500ns)<br> 2) DPPC_512_NaCl_150mM_320K (700ns)<br> 3) DPPC_512_NaCl_150mM_320K_v-rescale (500ns)<br> 4) DPPC_512_NaCl_150mM_322K_v-rescale (700ns)<br> 5) DPPC_512_NaCl_150mM_325K (500ns)<br> 6) DPPC_512_NaCl_150mM_325K_v-rescale (500ns)<br> 7) DPPC_512_NaCl_150mM_325K_cutoff09 (500ns)<br> 8) DPPC_512_NaCl_150mM_325K_MEMB_338K (500ns)<br> 9) DPPC_512_NaCl_150mM_338K (500ns)</p> <p>For further information read the Readme file provided for each simulation.</p>
Set simulations small pure bilayers (72 lipids) using charmm36 ff in gromacs (DPPC, POPC)
<p>Collection simulations of DPPC and POPC bilayers in gromacs using the charmm36 force field. The list of systems describing their particular simulation conditions can be found below:</p> <p>1) DPPC_72_325K (500ns)<br> 2) DPPC_72_310K_rmcomm_leaflets (500ns)<br> 3) DPPC_72_310K_rmcomm_leaflets_low_hydration (500ns)<br> 4) POPC_72_310K (500ns)<br> 5) POPC_72_310K_rmcomm_leaflets (500ns)<br> 6) POPC_72_310K_rmcomm_leaflets_low_hydration (550ns)<br> 7) POPC_72_303K_rmcomm_leaflets_low_hydration (550ns)</p> <p>For further information read the Readme file provided for each simulation.</p>
Simulations of POPC bilayers and monolayers at three different sizes. CHARMM36 with OPC water model
<p>Simulations of POPC bilayers and monolayers with the CHARMM36 force field and OPC water. Three system sizes are used: small ("s", 64 lipids), medium ("m", 256 lipids), and large ("l", 1024 lipids). All simulations are 1 µs long. The simulations are performed using GROMACS, and for each system the following are provided for bilayers (without "mono" in the name) and monolayers (with "mono" in the name):</p> <ul> <li>run input file (tpr)</li> <li>energy file (edr)</li> <li>trajectory file (xtc)</li> <li>checkpoint file (cpt) </li> <li>final structure (gro)</li> </ul> <p>Additionally, the following are shared by the monolayer and bilayer, and their naming convention follows the bilayer one.</p> <ul> <li>index file (ndx)</li> <li>topology file (top)</li> </ul> <p>The simulation parameter files (mdp) are provided separately for bilayers and monolayers. The molecular topologies (top) are included in TOP.tar.</p> <p>The CHARMM36 force field is obtained from http://mackerell.umaryland.edu/charmm_ff.shtml</p>
Simulations of OMPC, SOPC, and DOPC bilayers and monolayers at three different sizes. CHARMM36 with OPC water model
<p>Simulations of OMPC, SOPC, and DOPC bilayers and monolayers with the CHARMM36 force field and OPC water. Three system sizes are used: small ("s", 64 lipids), medium ("m", 256 lipids), and large ("l", 1024 lipids). All simulations are 1 µs long. The simulations are performed using GROMACS, and for each system the following are provided for bilayers ("BIL") and monolayers ("MONO"), separated into two tar archives, one for bilayers and one for monolayers.</p> <ul> <li>run input file (tpr)</li> <li>energy file (edr)</li> <li>trajectory file (xtc)</li> <li>checkpoint file (cpt) </li> <li>final structure (gro)</li> </ul> <p>Additionally, the following are shared by the monolayer and bilayer, and are not included in the tar arcives.</p> <ul> <li>index file (ndx)</li> <li>topology file (top)</li> </ul> <p>The simulation parameter files (mdp) are provided separately for bilayers and monolayers. The molecular topologies (top) are included in TOP.tar.</p> <p>The CHARMM36 force field is obtained from http://mackerell.umaryland.edu/charmm_ff.shtml</p>
DPPC lipid bilayer simulation with CHARMM36-LJPME force field using OpenMM
<p>DPPC lipid bilayer simulation (300 ns) with CHARMM36-LJPME force field using OpenMM at 323K.</p> <p>Used in <a href="http://doi.org/10.1021/acs.jctc.1c00951">https://doi.org/10.1021/acs.jctc.1c00951</a></p> <p>The force field parameters were downloaded from <a href="https://terpconnect.umd.edu/%7Ejbklauda/ff.html">https://terpconnect.umd.edu/%7Ejbklauda/ff.html</a>.</p> <p><a href="https://zenodo.org/api/files/1e89f677-91a8-472d-aebb-144fddd58d23/trajCORRECT1-2.dcd?versionId=5317fd88-6b98-4905-b171-53c1cd199cfe">trajCORRECT1-2.dcd </a>has incorrect timestamps. traj1-2.xtc has correct timestamps.<br> </p>
Single lipid component membrane bilayer MD with CHARMM36 force field, simulated with the CHARMM program
<p>Data for ten single component lipid bilayer simulations, with 3 files per lipid: a DCD file with coordinates, a PSF file describing the system, and a .zip file containing the starting coordinate set (CHARMM COOR format) and the other inputs used for the CHARMM simulations. Only the POPG system includes ions: Na+ to neutralize the lipids, and ca. 0.15 M NaCl.</p> <p>The DCD trajectory files contain coordinate sets stored at 0.1 ns intervals, <br> and are in the original CHARMM binary format.</p> <p>Lipid Nlpd Nwat ns<br> DLPC 648 25920 200<br> DMPC 648 16632 100<br> DOPC 648 21681 350<br> DOPE 648 21681 350<br> DPPC 648 19701 300<br> POPC 648 20178 200<br> POPE 720 23049 100<br> POPG 648 29160 200<br> PSM 648 18828 200<br> SDPE 648 25920 100</p> <p>"Mechanical properties of lipid bilayers from molecular dynamics simulation",<br> R. M. Venable, F. L. Brown and R. W. Pastor,<br> Chemistry and Physics of Lipids, 192 pp. 60-74 (2015). </p> <p>https://pubmed.ncbi.nlm.nih.gov/26238099/<br> https://www.sciencedirect.com/science/article/pii/S0009308415300190?via%3Dihub</p> <p> See also:</p> <p>"Identifying systematic errors in a power spectral analysis of simulated<br> lipid membranes"<br> Muhammed F. Ergüder, Markus Deserno<br> J. Chem. Phys. 154, 214103 (2021); doi: 10.1063/5.0049448<br> </p> <p> </p>
DPPC/POPC/POPG/CHL1 Monolayer Simulations With Charmm36+OPC (Part 4/4)
<p>DPPC/POPC/POPG/CHL1 (60/20/10/10 mol-%) monolayers simulated at varying area per lipid and temperature in the NVT ensemble. The Charmm36 lipid model [1] is used together with the 4-point OPC water model [2]. Each system consist of two monolayers with 169, 676, or 1521 lipids each. The monolayers are separated by a water slab, and surrounded by vacuum.</p> <p>The numbering in the filenames corresponds to the area per lipid in Ångströms * 10, temperature, number of lipids per monolayer if not 169. The starting structures were generated with CHARMM-GUI with an initial area per lipid of 50 Å^2, followed by a simulation during which the monolayer area was either compressed or expanded using PLUMED.</p> <p>All trajectories are simulated for 1000 ns, except the 1521 lipid per monolayer systems for 500 ns, with Gromacs 5.1.x [3] using the default Charmm36 monolayer simulations parameters given in the mdp file. Topology (.top) and index files are also common for all simulations. The topologies (.itp) for the lipids can be obtained from Charmm-GUI and for the OPC water model from https://bioinformatics.cs.vt.edu/~izadi/ .</p> <p>Part 1 of this upload is available at: DOI:10.5281/zenodo.3898344</p> <p>Part 2 of this upload is available at: DOI:10.5281/zenodo.3899875</p> <p>Part 3 of this upload is available at: DOI:10.5281/zenodo.3899535</p> <p>Part 4 of this upload is available at: DOI:10.5281/zenodo.4034250</p> <p>Juho Liekkinen, Berta de Santos Moreno, Riku O. Paananen, Ilpo Vattulainen, Luca Monticelli, Jorge Bernardino de la Serna, and Matti Javanainen. Understanding the Functional Properties of Lipid Heterogeneity in Pulmonary Surfactant Monolayers at the Atomistic Level. Frontiers in Cell and Developmental Biology - Cellular Biochemistry (2020)</p> <p>doi: 10.3389/fcell.2020.581016</p> <p>[1] DOI: 10.1021/jp101759q</p> <p>[2] DOI: 10.1021/jz501780a</p> <p>[3] DOI: 10.1016/j.softx.2015.06.001</p>
DPPC/POPC/POPG/CHL1 Monolayer Simulations With Charmm36+OPC (Part 2/4)
<p>DPPC/POPC/POPG/CHL1 (60/20/10/10 mol-%) monolayers simulated at varying area per lipid and temperature in the NVT ensemble. The Charmm36 lipid model [1] is used together with the 4-point OPC water model [2]. Each system consist of two monolayers with 169 lipids each. The monolayers are separated by a water slab, and surrounded by vacuum.</p> <p>The numbering in the filenames corresponds to the area per lipid in Ångströms * 10, temperature, possible independent repetitions (2 and 3). The starting structures were generated with CHARMM-GUI with an initial area per lipid of 50 Å^2, followed by a simulation during which the monolayer area was either compressed or expanded using PLUMED.</p> <p>All trajectories are simulated for 1000 ns with Gromacs 5.1.x [3] using the default Charmm36 monolayer simulations parameters given in the mdp file. Topology (.top) and index files are also common for all simulations. The topologies (.itp) for the lipids can be obtained from Charmm-GUI and for the OPC water model from https://bioinformatics.cs.vt.edu/~izadi/ .</p> <p>Part 1 of this upload is available at: DOI:10.5281/zenodo.3898344</p> <p>Part 2 of this upload is available at: DOI:10.5281/zenodo.3899875</p> <p>Part 3 of this upload is available at: DOI:10.5281/zenodo.3899535</p> <p>Part 4 of this upload is available at: DOI:10.5281/zenodo.4034250</p> <p>Juho Liekkinen, Berta de Santos Moreno, Riku O. Paananen, Ilpo Vattulainen, Luca Monticelli, Jorge Bernardino de la Serna, and Matti Javanainen. Understanding the Functional Properties of Lipid Heterogeneity in Pulmonary Surfactant Monolayers at the Atomistic Level. Frontiers in Cell and Developmental Biology - Cellular Biochemistry (2020)</p> <p>doi: 10.3389/fcell.2020.581016</p> <p>[1] DOI: 10.1021/jp101759q</p> <p>[2] DOI: 10.1021/jz501780a</p> <p>[3] DOI: 10.1016/j.softx.2015.06.001</p>
DPPC/POPC/POPG/CHL1 Monolayer Simulations With Charmm36+OPC (Part 1/4)
<p>DPPC/POPC/POPG/CHL1 (60/20/10/10 mol-%) monolayers simulated at varying area per lipid and temperature in the NVT ensemble. The Charmm36 lipid model [1] is used together with the 4-point OPC water model [2]. Each system consist of two monolayers with 169 lipids each. The monolayers are separated by a water slab, and surrounded by vacuum.</p> <p>The numbering in the filenames corresponds to the area per lipid in Ångströms * 10, temperature, possible independent repetitions (2 and 3). The starting structures were generated with CHARMM-GUI with an initial area per lipid of 50 Å^2, followed by a simulation during which the monolayer area was either compressed or expanded using PLUMED.</p> <p>All trajectories are simulated for 1000 ns with Gromacs 5.1.x [3] using the default Charmm36 monolayer simulations parameters given in the mdp file. Topology (.top) and index files are also common for all simulations. The topologies (.itp) for the lipids can be obtained from Charmm-GUI and for the OPC water model from https://bioinformatics.cs.vt.edu/~izadi/ .</p> <p>Part 1 of this upload is available at: DOI:10.5281/zenodo.3898344</p> <p>Part 2 of this upload is available at: DOI:10.5281/zenodo.3899875</p> <p>Part 3 of this upload is available at: DOI:10.5281/zenodo.3899535</p> <p>Part 4 of this upload is available at: DOI:10.5281/zenodo.4034250</p> <p>Juho Liekkinen, Berta de Santos Moreno, Riku O. Paananen, Ilpo Vattulainen, Luca Monticelli, Jorge Bernardino de la Serna, and Matti Javanainen. Understanding the Functional Properties of Lipid Heterogeneity in Pulmonary Surfactant Monolayers at the Atomistic Level. Frontiers in Cell and Developmental Biology - Cellular Biochemistry (2020)</p> <p>doi: 10.3389/fcell.2020.581016</p> <p>[1] DOI: 10.1021/jp101759q</p> <p>[2] DOI: 10.1021/jz501780a</p> <p>[3] DOI: 10.1016/j.softx.2015.06.001</p>
DPPC/POPC/POPG/CHL1 Monolayer Simulations With Charmm36+OPC (Part 3/4)
<p>DPPC/POPC/POPG/CHL1 (60/20/10/10 mol-%) monolayers simulated at varying area per lipid and temperature in the NVT ensemble. The Charmm36 lipid model [1] is used together with the 4-point OPC water model [2]. Each system consist of two monolayers with 169 lipids each. The monolayers are separated by a water slab, and surrounded by vacuum.</p> <p>The numbering in the filenames corresponds to the area per lipid in Ångströms * 10, temperature, possible independent repetitions (2 and 3). The starting structures were generated with CHARMM-GUI with an initial area per lipid of 50 Å^2, followed by a simulation during which the monolayer area was either compressed or expanded using PLUMED.</p> <p>All trajectories are simulated for 1000 ns with Gromacs 5.1.x [3] using the default Charmm36 monolayer simulations parameters given in the mdp file. Topology (.top) and index files are also common for all simulations. The topologies (.itp) for the lipids can be obtained from Charmm-GUI and for the OPC water model from https://bioinformatics.cs.vt.edu/~izadi/ .</p> <p>Part 1 of this upload is available at: DOI:10.5281/zenodo.3898344</p> <p>Part 2 of this upload is available at: DOI:10.5281/zenodo.3899875</p> <p>Part 3 of this upload is available at: DOI:10.5281/zenodo.3899535</p> <p>Part 4 of this upload is available at: DOI:10.5281/zenodo.4034250</p> <p>Juho Liekkinen, Berta de Santos Moreno, Riku O. Paananen, Ilpo Vattulainen, Luca Monticelli, Jorge Bernardino de la Serna, and Matti Javanainen. Understanding the Functional Properties of Lipid Heterogeneity in Pulmonary Surfactant Monolayers at the Atomistic Level. Frontiers in Cell and Developmental Biology - Cellular Biochemistry (2020)</p> <p>doi: 10.3389/fcell.2020.581016</p> <p>[1] DOI: 10.1021/jp101759q</p> <p>[2] DOI: 10.1021/jz501780a</p> <p>[3] DOI: 10.1016/j.softx.2015.06.001</p>
MD simulation trajectory and related files for POPC bilayer (CHARMM36, Gromacs 4.5)
<p>Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, CHARMM36 force field (dx.doi.org/10.1021/jp101759q), 20ns, T=303K, 72 POPC molecules, 2242 water molecules. This data is ran for the nmrlipids.blospot.fi project. More details from nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi. If data is used, please cite nmrlipids.blogspot.fi project and the original publication of the parameters (dx.doi.org/10.1021/jp101759q).</p>
MD simulation trajectory and related files for POPC bilayer in low hydration (CHARMM36, Gromacs 4.5)
<p>Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, CHARMM36 force field in low hydration (dx.doi.org/10.1021/jp101759q), 20ns, T=303K, 72 POPC molecules, 504 water molecules. This data is ran for the nmrlipids.blospot.fi project. More details from nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi. If data is used, please cite nmrlipids.blogspot.fi project and the original publication of the parameters (dx.doi.org/10.1021/jp101759q).</p>
MD simulation trajectory for POPC/50% Chol bilayer (CHARMM36, Gromacs 4.5)
<p>Equilibrated POPC/50%CHL lipid bilayer ran with Gromacs 4.5 with CHARMM36 lipid forcefield.<br /> The simulation is composed of 80 POPC/80 Cholesterol at full hydratation and ran for 200ns at 303K, data saved every 20ps.<br /> All input parameters can be find on the github repository: https://github.com/NMRLipids/nmrlipids.blogspot.fi</p> <p>This data is used in the project "Matching lipid force fields with NMR data". More information at : http://nmrlipids.blogspot.fi/</p>
MD simulation trajectory and related files for POPC bilayer (CHARMM36, Gromacs 4.5)
<p>Equilibrated POPC lipid bilayer ran with Gromacs 4.5 with CHARMM36 lipid forcefield.<br /> The simulation is composed of 128 POPC at full hydratation and ran for 200ns at 303K, data saved every 20ps.<br /> All input parameters can be find on the github repository: https://github.com/NMRLipids/nmrlipids.blogspot.fi</p> <p>This data is used in the project "Matching lipid force fields with NMR data". More information at : http://nmrlipids.blogspot.fi/</p>
MD simulation trajectory for POPC/20% Chol bilayer (CHARMM36, Gromacs 4.5)
<p>Equilibrated POPC/20%CHL lipid bilayer ran with Gromacs 4.5 with CHARMM36 lipid forcefield.<br /> The simulation is composed of 100 POPC/24 Cholesterol at full hydratation and ran for 200ns at 303K, data saved every 20ps.<br /> All input parameters can be find on the github repository: https://github.com/NMRLipids/nmrlipids.blogspot.fi</p> <p>This data is used in the project "Matching lipid force fields with NMR data". More information at : http://nmrlipids.blogspot.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>
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