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158 results for “Charmm36”
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>
POPC @ 310K, 450 mM of CaCl_2. Charmm36 with ECC-scaled ions
<p>Simulations of a POPC bilayer with 450 mM of CaCl_2. <br> 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> <p>A POPC bilayer consisting of 200 lipids (100 per leaflet) <br> is simulated in the presence of 450 mM CaCl_2. The Charmm36 <br> model is employed for lipids, the Charmm compatible variant <br> of the tip3p model for water, and the recent ion parameters <br> by Kohagen et al. [2] for CaCl_2.</p> <p>The Charmm36 force field parameters were obtained from<br> CHARMM-GUI [3] at http://www.charmm-gui.org</p> <p>The ion parameters are available at<br> https://bitbucket.org/hseara/ions/</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>The files are in GROMACS format. Trajectory (.xtc) is <br> 100 ns long with data saved every 100 ps. These data<br> were collected once the adsorption and desorption of <br> CaCl_2 to the surface has reached equilibrium, namely<br> after 700 ns of simulation. Additionally, the initial <br> structure (.gro), topology (.top), index file (.ndx), <br> simulation paremeter file (.mdp), binary run input file <br> for GROMACS v. 5.0–> (.tpr) and the energy output file <br> (.edr) are provided. </p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>[1] Update of the CHARMM All-Atom Additive Force Field <br> for Lipids: Validation on Six Lipid Types<br> Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, <br> Joseph W. O’Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, <br> Igor Vorobyov, Alexander D. MacKerell, Jr., and Richard W. Pastor<br> The Journal of Physical Chemistry B 2010 114 (23), 7830-7843<br> DOI: 10.1021/jp101759q</p> <p>[2] Accurate Description of Calcium Solvation in Concentrated Aqueous Solutions<br> Miriam Kohagen, Philip E. Mason, and Pavel Jungwirth<br> The Journal of Physical Chemistry B 2014 118 (28), 7902-7909<br> DOI: 10.1021/jp5005693</p> <p>[3] CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, <br> and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field<br> Jumin Lee, Xi Cheng, Jason M. Swails, Min Sun Yeom, Peter K. Eastman, <br> Justin A. Lemkul, Shuai Wei, Joshua Buckner, Jong Cheol Jeong, Yifei Qi, <br> Sunhwan Jo, Vijay S. Pande, David A. Case, Charles L. Brooks, III, <br> Alexander D. MacKerell, Jr., Jeffery B. Klauda, and Wonpil Im<br> Journal of Chemical Theory and Computation 2016 12 (1), 405-413<br> DOI: 10.1021/acs.jctc.5b00935</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>
POPC @ 310K, 450 mM of CaCl_2. Charmm36 with default Charmm ions
<p>Simulations of a POPC bilayer with 450 mM of CaCl_2. <br> 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> <p>A POPC bilayer consisting of 200 lipids (100 per leaflet) <br> is simulated in the presence of 450 mM CaCl_2. The Charmm36 <br> model [1] is employed for lipids, the Charmm compatible variant <br> of the tip3p model for water, and the default Charmm<br> ion parameters (type CAL) for CaCl_2.</p> <p>The Charmm36 force field parameters were obtained from http://mackerell.umaryland.edu/charmm_ff.shtml</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>The files are in GROMACS format. Trajectory (.xtc) is <br> 100 ns long with data saved every 100 ps. These data<br> were collected after 1900 ns of simulation Additionally,</p> <p>the initial structure (.gro), topology (.top), index file (.ndx), <br> simulation paremeter file (.mdp), binary run input file <br> for GROMACS v. 5.0–> (.tpr) and the energy output file <br> (.edr) are provided. </p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>[1] Update of the CHARMM All-Atom Additive Force Field <br> for Lipids: Validation on Six Lipid Types<br> Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, <br> Joseph W. O’Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, <br> Igor Vorobyov, Alexander D. MacKerell, Jr., and Richard W. Pastor<br> The Journal of Physical Chemistry B 2010 114 (23), 7830-7843<br> DOI: 10.1021/jp101759q</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>
POPC with 0, 10, 20, and 30 mol-% of cholesterol at 310 K. Charmm36 force field. *OBSOLETE*
<p>A POPC bilayer consisting of 200 lipids (100 per leaflet) <br> is simulated in the presence of 0% (0 molecules), 10 %<br> (22 molecules), 20 % (50 molecules), or 30 % (86 molecules)<br> of cholesterol. The Charmm36 model [1] is employed for lipids and the Charmm-compatible variant of the tip3p model for water.</p> <p>The Charmm36 force field parameters were obtained from CHARMM-GUI [2] at http://www.charmm-gui.org</p> <p> </p> <p>*** IMPORTANT ***</p> <p>These simulations were performed using an erroneous charmm36.itp file provided by version 1.7 of CHARMM-GUI, as stated in http://www.charmm-gui.org/?doc=log : "The multiplicity (of dihedral parameters) issue in GROMACS inputs; this issue affects the systems generated from August 21<sup>th</sup> 2015 to December 9<sup>th</sup> 2015." Due to the bad .itp, the deuterium order parameters of C2, as well as the glycerol group, show strange behavior. The systems simulated with the correct itp file can be accessed at: DOI: 10.5281/zenodo.159759.</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>The files are in GROMACS format. Trajectory (.xtc) is 100 ns long with data saved every 100 ps. Additionally, the initial structure (.gro), topology (.top), index file (.ndx), simulation paremeter file (.mdp), binary run input file for GROMACS v. 5.0–> (.tpr) and the energy output file (.edr) are provided. </p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>[1] Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types</p> <p>Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, Joseph W. O’Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, Igor Vorobyov, Alexander D. MacKerell, Jr., and Richard W. Pastor</p> <p>The Journal of Physical Chemistry B 2010 114 (23), 7830-7843</p> <p>DOI: 10.1021/jp101759q</p> <p> </p> <p>[2] CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field</p> <p>Jumin Lee, Xi Cheng, Jason M. Swails, Min Sun Yeom, Peter K. Eastman, Justin A. Lemkul, Shuai Wei, Joshua Buckner, Jong Cheol Jeong, Yifei Qi, Sunhwan Jo, Vijay S. Pande, David A. Case, Charles L. Brooks, III, Alexander D. MacKerell, Jr., Jeffery B. Klauda, and Wonpil Im</p> <p>Journal of Chemical Theory and Computation 2016 12 (1), 405-413</p> <p>DOI: 10.1021/acs.jctc.5b00935</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>
POPC monolayer simulations with Charmm36+OPC @ 323 K
<p>POPC monolayers simulated at a varying area per lipid in the NVT ensemble. The Charmm36 lipid model [1] is employed together with the 4-point OPC water model [2].</p> <p>Each system contains two monolayers with 64 lipids each, except for the system '120large', which contains 256 lipids per monolayer. These monolayers are separated by a water slab, and surrounded by vacuum. </p> <p>The number in the filename corresponds to the area per lipid in Ångströms. The starting structures were taken from [3], which also provides detailed information on system setup. The simulations in [3] used TIP3P water and Slipids lipids, which were replaced by OPC water and Charmm36 lipids, followed by energy minimization and production runs.</p> <p>All trajectories, 100 ns long, are simulated with Gromacs 5.0.x [4] using the parameters given in the mdp file. The topologies for the lipids can be obtained from Charmm-GUI and for the OPC water model from https://bioinformatics.cs.vt.edu/~izadi/ .</p> <p>Note that .top and .ndx files are for all systems except for the "120large".</p> <p>[1] DOI: 10.1021/jp101759q<br> [2] DOI: 10.1021/jz501780a<br> [3] DOI: 10.1016/j.bbamem.2016.09.015<br> [4] DOI: 10.1016/j.softx.2015.06.001</p>
DPPC monolayer simulations with Charmm36+OPC @ 323 K
<p>DPPC monolayers simulated at a varying area per lipid in the NVT ensemble. The Charmm36 lipid model [1] is employed together with the 4-point OPC water model [2].</p> <p>Each system contains two monolayers with 64 lipids each with a change in simulation box size, except for the system titled 'large'. '200large' contains 128 lipids per monolayer, '400large' 64 lipids per monolayer and '1500large' 17 lipids per monolayer. These 'large' monolayers all have the same simulation box size. All monolayers are separated by a water slab, and surrounded by vacuum. </p> <p>The number in the filename corresponds to the area per lipid in Ångströms. The starting structures were taken from [4], which also provides detailed information on system setup. The simulations in [3] used Slipids lipid model and TIP3P water model, which were replaced by Charmm36 lipid model and the OPC water model, followed by energy minimization and production runs. The 'large' monolayers were generated from the system 'md100' by replicating it four-fold (2x2) and subsequently removing lipids until the desired area per lipid was reached.</p> <p>All trajectories, 100 ns long, are simulated with Gromacs 5.0.x [4] using the parameters given in the mdp file. The topologies for the lipids can be obtained from Charmm-GUI and for the OPC water model from https://bioinformatics.cs.vt.edu/~izadi/ .</p> <p>[1] DOI: 10.1021/jp101759q<br> [2] DOI: 10.1021/jz501780a<br> [3] DOI: 10.1016/j.bbamem.2016.09.015<br> [4] DOI: 10.1016/j.softx.2015.06.001</p>
POPC monolayer simulations with Charmm36+TIP(S)3P @ 310 K
<p>POPC monolayers simulated at a varying area per lipid in the NVT ensemble. The Charmm36 lipid model [1] is employed together with the Charmm-specific TIP3P (TIPS3P) water model.</p> <p>Each system contains two monolayers with 64 lipids each. These monolayers are separated by a water slab, and surrounded by vacuum. </p> <p>The number in the filename corresponds to the area per lipid in Ångströms. The starting structures were taken from [2], which also provides detailed information on system setup. The simulations in [2] used TIP3P water and Slipids lipids, which were replaced by TIPS3P water and Charmm36 lipids, followed by energy minimization and production runs.</p> <p>All trajectories, 100 ns long, are simulated with Gromacs 5.0.x [3] using the parameters given in the mdp file. The topologies for the lipids can be obtained from Charmm-GUI.</p> <p>[1] DOI: 10.1021/jp101759q<br> [2] DOI: 10.1016/j.bbamem.2016.09.015<br> [3] DOI: 10.1016/j.softx.2015.06.001</p>
POPC monolayer simulations with Charmm36+OPC @ 310 K
<p>POPC monolayers simulated at a varying area per lipid in the NVT ensemble. The Charmm36 lipid model [1] is employed together with the 4-point OPC water model [2].</p> <p>Each system contains two monolayers with 64 lipids each. These monolayers are separated by a water slab, and surrounded by vacuum. </p> <p>The number in the filename corresponds to the area per lipid in Ångströms. The starting structures were taken from [3], which also provides detailed information on system setup. The simulations in [3] used TIP3P water and Slipids lipids, which were replaced by OPC water and Charmm36 lipids, followed by energy minimization and production runs.</p> <p>All trajectories, 100 ns long, are simulated with Gromacs 5.0.x [4] using the parameters given in the mdp file. The topologies for the lipids can be obtained from Charmm-GUI and for the OPC water model from https://bioinformatics.cs.vt.edu/~izadi/ .</p> <p>[1] DOI: 10.1021/jp101759q<br> [2] DOI: 10.1021/jz501780a<br> [3] DOI: 10.1016/j.bbamem.2016.09.015<br> [4] DOI: 10.1016/j.softx.2015.06.001</p>
DPPC monolayer simulations with Charmm36+TIP(S)3P @ 310 K
<p>POPC monolayers simulated at a varying area per lipid in the NVT ensemble. The Charmm36 lipid model [1] is employed together with the Charmm-specific TIP3P (TIPS3P) water model.</p> <p>Each system contains two monolayers with 64 lipids each. These monolayers are separated by a water slab, and surrounded by vacuum. </p> <p>The number in the filename corresponds to the area per lipid in Ångströms. The starting structures were taken from [2], which also provides detailed information on system setup. The simulations in [2] used TIP3P water and Slipids lipids, which were replaced by TIPS3P water and Charmm36 lipids, followed by energy minimization and production runs.</p> <p>All trajectories, 100 ns long, are simulated with Gromacs 5.0.x [3] using the parameters given in the mdp file. The topologies for the lipids can be obtained from Charmm-GUI.</p> <p>[1] DOI: 10.1021/jp101759q<br> [2] DOI: 10.1016/j.bbamem.2016.09.015<br> [3] DOI: 10.1016/j.softx.2015.06.001</p>
DPPC monolayer simulations with Charmm36+OPC @ 310 K
<p>POPC monolayers simulated at a varying area per lipid in the NVT ensemble. The Charmm36 lipid model [1] is employed together with the 4-point OPC water model [2].</p> <p>Each system contains two monolayers with 64 lipids each. These monolayers are separated by a water slab, and surrounded by vacuum. </p> <p>The number in the filename corresponds to the area per lipid in Ångströms. The starting structures were taken from [3], which also provides detailed information on system setup. The simulations in [3] used TIP3P water and Slipids lipids, which were replaced by OPC water and Charmm36 lipids, followed by energy minimization and production runs.</p> <p>All trajectories, 100 ns long, are simulated with Gromacs 5.0.x [4] using the parameters given in the mdp file. The topologies for the lipids can be obtained from Charmm-GUI and for the OPC water model from https://bioinformatics.cs.vt.edu/~izadi/ </p> <p>[1] DOI: 10.1021/jp101759q<br> [2] DOI: 10.1021/jz501780a<br> [3] DOI: 10.1016/j.bbamem.2016.09.015<br> [4] DOI: 10.1016/j.softx.2015.06.001</p>
POPC with varying amounts of cholesterol, 450 mM of CaCl_2. Charmm36 with default Charmm ions
<p>Simulations of a POPC bilayer with varying amounts (0, 10, 20, and 30 mol-%) of cholesterol and 450 mM of CaCl_2 performed at 310 K. The POPC bilayer consists of 200 lipids (100 per leaflet) and on top of that there is 0 (0%), 22 (10%), 50 (20%), or 86 (30%) of cholesterol. The Charmm36 model [1,2] is employed for lipids, the Charmm compatible variant of the tip3p model for water, and the default Charmm ion parameters (type CAL) for CaCl_2.</p> <p>The Charmm36 force field parameters were obtained from http://mackerell.umaryland.edu/charmm_ff.shtml .<br> ––––––––––––––––––––––––––––––––––––––––––––––––––––––<br> The files are in GROMACS format and named based on the amount of cholesterol present (in %) in the corresponding simulation. Trajectories (.xtc) are 2 µs long with data saved every 100 ps. Additionally, the final structure (.gro), topology (.top), index file (.ndx), energy output file (.edr), and binary run input files (for Gromacs 5.0->) (.tpr) are provided for each system. The common simulation parameter file (.mdp) is also provided.<br> ––––––––––––––––––––––––––––––––––––––––––––––––––––––<br> [1] Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types. Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, Joseph W. O’Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, Igor Vorobyov, Alexander D. MacKerell, Jr., and Richard W. Pastor, The Journal of Physical Chemistry B 2010 114 (23), 7830–7843, DOI: 10.1021/jp101759q</p> <p>[2] Update of the Cholesterol Force Field Parameters in CHARMM. Joseph B. Lim, Brent Rogaski, and Jeffery B. Klauda, The Journal of Physical Chemistry B 2012 116 (1), 203–210, DOI: 10.1021/jp207925m</p>
POPC with varying amounts of cholesterol, 450 mM of CaCl_2. Charmm36 with ECC-scaled ions
<p>Simulations of a POPC bilayer with varying amounts (0, 10, 20, and 30 mol-%) of cholesterol and 450 mM of CaCl_2 performed at 310 K. The POPC bilayer consists of 200 lipids (100 per leaflet) and on top of that there is 0 (0%), 22 (10%), 50 (20%), or 86 (30%) of cholesterol. The Charmm36 model [1,2] is employed for lipids, the Charmm compatible variant of the tip3p model for water, and the recent ion parameters by Kohagen et al. [3] for CaCl_2.</p> <p>The Charmm36 force field parameters were obtained Charmm-GUI [4], and the ion parameters are available at https://bitbucket.org/hseara/ions/ . IMPORTANT: The simulations are performed with version 1.7 obtained from Charmm-GUI, and this version is known to have an issue with the multiplicity of dihedrals in Gromacs output files, see http://www.charmm-gui.org/?doc=log . <br> ––––––––––––––––––––––––––––––––––––––––––––––––––––––<br> The files are in GROMACS format and named based on the amount of cholesterol present (in %) in the corresponding simulation. Trajectories (.xtc) are 800 ns long with data saved every 100 ps. Additionally, the final structure (.gro), topology (.top), index file (.ndx), energy output file (.edr), and binary run input files (for Gromacs 5.0->) (.tpr) are provided for each system. The common simulation parameter file (.mdp) is also provided.<br> ––––––––––––––––––––––––––––––––––––––––––––––––––––––<br> [1] Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types. Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, Joseph W. O’Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, Igor Vorobyov, Alexander D. MacKerell, Jr., and Richard W. Pastor, The Journal of Physical Chemistry B 2010 114 (23), 7830–7843, DOI: 10.1021/jp101759q</p> <p>[2] Update of the Cholesterol Force Field Parameters in CHARMM. Joseph B. Lim, Brent Rogaski, and Jeffery B. Klauda, The Journal of Physical Chemistry B 2012 116 (1), 203–210, DOI: 10.1021/jp207925m</p> <p>[3] Accurate Description of Calcium Solvation in Concentrated Aqueous Solutions. Miriam Kohagen, Philip E. Mason, and Pavel Jungwirth, The Journal of Physical Chemistry B 2014 118 (28), 7902-7909, DOI: 10.1021/jp5005693</p> <p>[4] CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field. Jumin Lee, Xi Cheng, Jason M. Swails, Min Sun Yeom, Peter K. Eastman, Justin A. Lemkul, Shuai Wei, Joshua Buckner, Jong Cheol Jeong, Yifei Qi, Sunhwan Jo, Vijay S. Pande, David A. Case, Charles L. Brooks, III, <br> Alexander D. MacKerell, Jr., Jeffery B. Klauda, and Wonpil Im, Journal of Chemical Theory and Computation 2016 12 (1), 405-413, DOI: 10.1021/acs.jctc.5b00935</p>
POPC with varying amounts of cholesterol, 130 mM of NaCl. Charmm36 with default Charmm ions
<p>Simulations of a POPC bilayer with varying amounts (0, 10, 20, and 30 mol-%) of cholesterol and 130 mM of NaCl performed at 310 K. The POPC bilayer consists of 200 lipids (100 per leaflet) and on top of that there is 0 (0%), 22 (10%), 50 (20%), or 86 (30%) of cholesterol. The Charmm36 model [1,2] is employed for lipids, the Charmm compatible variant of the tip3p model for water, and the standard Charmm ion parameters for NaCl [3].</p> <p>The Charmm36 force field parameters were obtained Charmm-GUI [4]. IMPORTANT: The simulations are performed with version 1.7 obtained from Charmm-GUI, and this version is known to have an issue with the multiplicity of dihedrals in Gromacs output files, see http://www.charmm-gui.org/?doc=log . <br> ––––––––––––––––––––––––––––––––––––––––––––––––––––––<br> The files are in GROMACS format and named based on the amount of cholesterol present (in %) in the corresponding simulation. Trajectories (.xtc) are 200 ns long with data saved every 100 ps. Additionally, the final structure (.gro), topology (.top), index file (.ndx), energy output file (.edr), and binary run input files (for Gromacs 5.0->) (.tpr) are provided for each system. The common simulation parameter file (.mdp) is also provided.<br> ––––––––––––––––––––––––––––––––––––––––––––––––––––––<br> [1] Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types. Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, Joseph W. O’Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, Igor Vorobyov, Alexander D. MacKerell, Jr., and Richard W. Pastor, The Journal of Physical Chemistry B 2010 114 (23), 7830–7843, DOI: 10.1021/jp101759q</p> <p>[2] Update of the Cholesterol Force Field Parameters in CHARMM. Joseph B. Lim, Brent Rogaski, and Jeffery B. Klauda, The Journal of Physical Chemistry B 2012 116 (1), 203–210, DOI: 10.1021/jp207925m</p> <p>[3] Control of Ion Selectivity in LeuT: Two Na+ Binding Sites with Two Different Mechanisms. Sergei Y. Noskov and Benoit Roux, Journal of Molecular Biology 2008 377 (3), 804–818, DOI:10.1016/j.jmb.2008.01.015</p> <p>[4] CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field. Jumin Lee, Xi Cheng, Jason M. Swails, Min Sun Yeom, Peter K. Eastman, Justin A. Lemkul, Shuai Wei, Joshua Buckner, Jong Cheol Jeong, Yifei Qi, Sunhwan Jo, Vijay S. Pande, David A. Case, Charles L. Brooks, III, <br> Alexander D. MacKerell, Jr., Jeffery B. Klauda, and Wonpil Im, Journal of Chemical Theory and Computation 2016 12 (1), 405-413, DOI: 10.1021/acs.jctc.5b00935</p>
Large POPC monolayer simulations with Charmm36+OPC @ 298 K (Part 1/2)
<p>POPC monolayers simulated at a varying area per lipid in the NVT ensemble. The Charmm36 lipid model [1] is employed together with the 4-point OPC water model [2]. Each system contains two monolayers with 256 lipids each. These monolayers are separated by a water slab, and surrounded by vacuum. </p> <p>The number in the filename corresponds to the area per lipid in Ångströms. The starting structures were generated by setting up a system with an area per lipid of 50 Å^2, followed by a simulation during which the monolayer area was expanded using PLUMED. </p> <p>All trajectories, 100 ns long, are simulated with Gromacs 5.0.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 2 of this upload is available at: https://doi.org/10.5281/zenodo.838633</p> <p>Matti Javanainen, Antti Lamberg, Lukasz Cwiklik, Ilpo Vattulainen, and O. H. Samuli Ollila. <em>Atomistic Model for Nearly Quantitative Simulations of Langmuir Monolayers</em>, Langmuir <strong>2018</strong> 34 (7), 2565-2572, DOI: 10.1021/acs.langmuir.7b02855</p> <p>[1] DOI: 10.1021/jp101759q<br> [2] DOI: 10.1021/jz501780a<br> [3] DOI: 10.1016/j.softx.2015.06.001</p>
Large DPPC monolayer simulations with Charmm36+OPC @ 310 K (Part 1/2)
<p>DPPC monolayers simulated at a varying area per lipid in the NVT ensemble. The Charmm36 lipid model [1] is employed together with the 4-point OPC water model [2]. Each system contains two monolayers with 256 lipids each. These monolayers are separated by a water slab, and surrounded by vacuum. </p> <p>The number in the filename corresponds to the area per lipid in Ångströms. The starting structures were generated by setting up a POPC monolayer system with an area per lipid of 50 Å^2, followed by a simulation during which the monolayer area was expanded using PLUMED. Next, POPC was replaced by DPPC, and the systems were energy minimized. Systems with area smaller than 51 Å^2 were generated by compressing the DPPC monolayer system with PLUMED.</p> <p>All trajectories, 100–200 ns long (until convergence of surface tension), are simulated with Gromacs 5.0.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 2 of this upload is available at https://doi.org/10.5281/zenodo.838641</p> <p>Matti Javanainen, Antti Lamberg, Lukasz Cwiklik, Ilpo Vattulainen, and O. H. Samuli Ollila. <em>Atomistic Model for Nearly Quantitative Simulations of Langmuir Monolayers</em>, Langmuir <strong>2018</strong> 34 (7), 2565-2572, DOI: 10.1021/acs.langmuir.7b02855</p> <p>[1] DOI: 10.1021/jp101759q<br> [2] DOI: 10.1021/jz501780a<br> [3] DOI: 10.1016/j.softx.2015.06.001</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.