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CHARMM36 POPS simulations (versions 1 and 2) 298 K 1.0 nm LJ switching

CHARMM36 POPS simulations (298 K, starting structure from the CHARMM-GUI) performed with a 1.0 nm point at which to switch off the van der Waals interactions. Two different simulations generated with different starting velocities are provided (the files are named v1 and v2 for these different simulations). The trajectories contain only the data from 400-500 ns of the simulations (as per the analysis provided on the nmrlipids blog) and additionally they have been processed with trjconv -skip 10 to keep the upload small.

CHARMM36-UA POPS simulations (versions 1 and 2) 298 K 1.0 nm LJ switching

CHARMM36-UA POPS simulations (298 K, starting structure from the CHARMM-GUI) performed with a 1.0 nm point at which to switch off the van der Waals interactions. Two different simulations generated with different starting velocities are provided (the files are named v1 and v2 for these different simulations). The trajectories contain only the data from 400-500 ns of the simulations (as per the analysis provided on the nmrlipids blog) and additionally they have been processed with trjconv -skip 10 to keep the upload small.

Berger POPS simulations (versions 1 and 2) 298 K 1.0 nm cut-off

Berger POPS simulations (298 K, starting structure from the CHARMM-GUI with the appropriate hydrogen atoms removed) performed with 1.0 nm cut-offs and no long range dispersion correction. Two different simulations generated with different starting velocities are provided (the files are named v1 and v2 for these different simulations). The trajectories contain only the data from 400-500 ns of the simulations (as per the analysis provided on the nmrlipids blog) and additionally they have been processed with trjconv -skip 10 to keep the upload small.

GROMOS-CKP POPS simulations (versions 1 and 2) 298 K with Berger/Chiu NH3 charges and PME

GROMOS-CKP POPS simulations (298 K, starting structure from the CHARMM-GUI with the appropriate hydrogen atoms removed) performed with 1.4 nm cut-offs, PME and a long range dispersion correction. The charges for the NH3 part of the head group are the same as in the Berger PS simulations (originally taken from the Berger/Chiu PC head group). Two different simulations generated with different starting velocities are provided (the files are named v1 and v2 for these different simulations). The trajectories contain only the data from 400-500 ns of the simulations (as per the analysis provided on the nmrlipids blog) and additionally they have been processed with trjconv -skip 10 to keep the upload small.

opencc-by-4.0Sep 2024View details →

Code for GMD publication - Introducing Graupel Density Prediction in Weather Research and Forecasting (WRF) Double-Moment 6-Class (WDM6) Microphysics and Evaluation of the Modified Scheme During the ICE-POP Field Campaign

Code for GMD publication - Introducing Graupel Density Prediction in Weather Research and Forecasting (WRF) Double-Moment 6-Class (WDM6) Microphysics and Evaluation of the Modified Scheme During the ICE-POP Field Campaign In this repository, we include the source codes for WRF microphysics parameterization used in the GMD publication "Simulated Prognostic approach of graupel density in a bulk-type cloud microphysics scheme and evaluation during the ICE-POP field campaign." The revised WDM6 code, which predicts the graupel density and the original WDM6 code are uploaded.   Each code is modified so that detailed microphysical processes can be found in wrfout. Namelist files shows the namelist.input for each case. Furthermore, scripts for figures in the manuscript are included, along with wrfout files.

opencc-by-4.0Feb 2018View details →

CHARMM36 POPS simulations (versions 1 and 2) 298 K 1.0 nm LJ switching with K ions

CHARMM36 POPS simulations (298 K, starting structure from the CHARMM-GUI) performed with a 1.0 nm point at which to switch off the van der Waals interactions. Two different simulations generated with different starting velocities are provided (the files are named v1 and v2 for these different simulations). The trajectories contain only the data from 400-500 ns of the simulations (as per the analysis provided on the nmrlipids blog) and additionally they have been processed with trjconv -skip 10 to keep the upload small. These simulations were performed with K ions used to neutralise the system.

opencc-by-4.0Jun 2018View details →

MacRog POPS simulations (versions 1 and 2) 298 K with corrected PO not OP tails

MacRog POPS simulations (298 K, starting structure from the CHARMM-GUI) performed with 1.0 nm cut-offs, PME and a dispersion correction. Two simulations were performed with differently assigned random starting velocities. Note that unlike the original MacRog simulations, these have the correct PO and not OP tails.

Molecular dynamics simulations of lipid bilayers containing POPC and POPS with the lipid17 force field, NaCl and KCl salt concentrations

Classical molecular dynamics simulations of various mixtures of POPC:POPS lipid bilayers in water solution at various NaCl, KCl and CaCl2 concentrations, with Na+ counterions (and K+ counterions when noted with "_KCl" suffix). Lipid17 force field parameters used for lipids, TIP3p water model and Dang ions. The file names report the number of additional cations. simulations performed with Gromacs 2018.0 (*.xtc files) simulation length 1000 ns = 1 microsecond temperature 298 K Gromacs simulation setting is in the file npt_lipid_bilayer.mdp

Molecular dynamics simulations of lipid bilayers containing POPC and POPS with the lipid17 force field and ff99 ions

Classical molecular dynamics simulations of various mixtures of POPC:POPS lipid bilayers in water solution at various NaCl, KCl and CaCl2 concentrations, with Na+ counterions (and K+ counterions when noted with "_KCl" suffix). Lipid17 force field parameters used for lipids, TIP3p water model and ff99 ions. The file names report the number of additional cations. simulations performed with Gromacs 2018.0 (*.xtc files) simulation length 1000 ns = 1 microsecond temperature 298 K Gromacs simulation setting is in the file npt_lipid_bilayer.mdp

Molecular dynamics simulations of lipid bilayers containing POPC and POPS with the lipid17 force field, only counterions, and CaCl2 concentrations

Molecular dynamics simulations of lipid bilayers containing POPC and POPS (various mixtures) with ECC-lipids force field, and Na+ (K+) counterions

Classical molecular dynamics simulations of various mixtures of POPC:POPS lipid bilayers in water solution with only Na+ counterions (or with K+ counterions when noted with "_KCl" suffix). ECC-lipids force field parameters used for lipids, SPC/E water model and ECC-ions, all parameters available at <a href="https://github.com/jmelcr/ecc_lipids">https://github.com/jmelcr/ecc_lipids</a> simulations performed with Gromacs 2018.0 (*.xtc files) simulation length 1000 ns = 1 microsecond temperature 298 K Gromacs simulation setting is in the file npt_lipid_bilayer.mdp

Molecular dynamics simulations of lipid bilayers containing POPC and POPS (5:1) with ECC-lipids force field, and Na+ (K+) counterions at various CaCl2 additional concentrations

Classical molecular dynamics simulations of various mixtures of POPC:POPS lipid bilayers in water solution with Na+ counterions (or with K+ counterions when noted with "_KCl" suffix) and an additional concentration of CaCl2. The numbers in the file names denote the number of additional Ca2+ cations. ECC-lipids force field parameters used for lipids, SPC/E water model and ECC-ions, all parameters available at <a href="https://github.com/jmelcr/ecc_lipids">https://github.com/jmelcr/ecc_lipids</a> simulations performed with Gromacs 2018.0 (*.xtc files) simulation length 1000 ns = 1 microsecond temperature 298 K Simulations without additional salts are at a <a href="https://doi.org/10.5281/zenodo.1488094">separate deposit: 10.5281/zenodo.1488094</a>.

POPC:POPS (5:1) with 890 mM potassium simulation with CHARMM36 at 298K

POPC:POPS (5:1) with 890 mM potassium simulation with CHARMM36 at 298K. Trajectory 50-200ns. 110 POPC molecules, 22 POPS molecules, 4946 water molecules and 79 Na+ ions.

POPC:POPS (5:1) with 450 mM potassium simulation with CHARMM36 at 298K

POPC:POPS (5:1) with 450 mM potassium simulation with CHARMM36 at 298K. Trajectory 50-200ns. 110 POPC molecules, 22 POPS molecules, 4926 water molecules and 40 Na+ ions.

POPC:POPS (5:1) with 440 mM sodium simulation with CHARMM36 at 298K

POPC:POPS (5:1) with 440 mM sodium simulation with CHARMM36 at 298K. Trajectory 50-200ns. 110 POPC molecules, 22 POPS molecules, 4965 water molecules and 39 Na+ ions.

POPC:POPS (5:1) with 890 mM sodium simulation with CHARMM36 at 298K

POPC:POPS (5:1) with 890 mM sodium simulation with CHARMM36 at 298K. Trajectory 50-200ns. 110 POPC molecules, 22 POPS molecules, 4932 water molecules and 79 Na+ ions.

Molecular dynamics simulations of lipid bilayers containing POPC and POPS (5:1) with ECC-lipids force field, and Na+ (K+) counterions at various additional concentrations of NaCl and KCl

Classical molecular dynamics simulations of various mixtures of POPC:POPS lipid bilayers in water solution with Na+ counterions (or with K+ counterions when noted with "_KCl" suffix) and an additional concentration of NaCl or KCl. The numbers in the file names denote the number of additional cations. ECC-lipids force field parameters used for lipids, SPC/E water model and ECC-ions, all parameters are included in this repository in GROMACS format and are also available at <a href="https://github.com/jmelcr/ecc_lipids">https://github.com/jmelcr/ecc_lipids</a> simulations performed with Gromacs 2018.0 (*.xtc files) simulation length 1000 ns = 1 microsecond temperature 298 K Simulations without additional salts are at a <a href="https://doi.org/10.5281/zenodo.1488094">separate deposit: 10.5281/zenodo.1488094</a>.

opennotspecifiedMay 2003View details →

text-fig. 18. Skulls of a basal ornithischian (a) and three theropods (b-d) in palatal view, showing different states for several cranial characters. A, Lesothosaurus diagnostics; redrawn from Sereno (199lb). B, Allosaurus fragilis', redrawn from Madsen (1976). c, Daspletosaurus torosus; redrawn from Russell (1970). D, Oviraptor philoceratops; redrawn from Barsbold et al. (1990). Abbreviations: bsp, basisphenoid; bspr, basisphenoid recess; ch, internal choana; cp, cultriform process of the parasphenoid; ect, ectopterygoid; iptv, interpterygoid vacuity; j, jugal; m, maxilla; oc, occipital condyle; pal, palatine; pm, premaxilla; pop, paroccipital process; pt, pterygoid; q, quadrate; qj, quadratojugal; sof, suborbital fenestra; spf, subsidiary palatal fenestra; snf, subnarial foramen; stf, subtemporal fenestra; v, vomer. Scale bars represent 10 mm (a), 50 mm (d) and 100 mm (b-c). in The interrelationships and evolution of basal theropod dinosaurs

text-fig. 18. Skulls of a basal ornithischian (a) and three theropods (b-d) in palatal view, showing different states for several cranial characters. A, Lesothosaurus diagnostics; redrawn from Sereno (199lb). B, Allosaurus fragilis', redrawn from Madsen (1976). c, Daspletosaurus torosus; redrawn from Russell (1970). D, Oviraptor philoceratops; redrawn from Barsbold et al. (1990). Abbreviations: bsp, basisphenoid; bspr, basisphenoid recess; ch, internal choana; cp, cultriform process of the parasphenoid; ect, ectopterygoid; iptv, interpterygoid vacuity; j, jugal; m, maxilla; oc, occipital condyle; pal, palatine; pm, premaxilla; pop, paroccipital process; pt, pterygoid; q, quadrate; qj, quadratojugal; sof, suborbital fenestra; spf, subsidiary palatal fenestra; snf, subnarial foramen; stf, subtemporal fenestra; v, vomer. Scale bars represent 10 mm (a), 50 mm (d) and 100 mm (b-c).

opennotspecifiedMay 2003View details →

text-fig. 16. Ventral view of the braincase, showing different states for characters 56 and 57. a, basal ornithischian Lesothosaurus diagnostics; based on Sereno (1991b). B, Syntarsus rhodesiensis based on QG 195; the postorbital processes of the laterosphenoid are broken in this specimen of Syntarsus; their attachments are placed above and slightly posterior to the trigeminal foramen. Abbreviations: boc, basioccipital; bpt, basipterygoid process; bsp, basisphenoid; bspr, basisphenoid recess; bt, basal tuber; fo, fenestra ovalis; Is, laterosphenoid; oc, occipital condyle; op, opisthotic; pop, paroccipital process; popls, postorbital process of the laterosphenoid; psp, parasphenoid; Roman numbers refer to the foramina for the exits of cranial nerves. Scale bars represent 10 mm. in The interrelationships and evolution of basal theropod dinosaurs

text-fig. 16. Ventral view of the braincase, showing different states for characters 56 and 57. a, basal ornithischian Lesothosaurus diagnostics; based on Sereno (1991b). B, Syntarsus rhodesiensis based on QG 195; the postorbital processes of the laterosphenoid are broken in this specimen of Syntarsus; their attachments are placed above and slightly posterior to the trigeminal foramen. Abbreviations: boc, basioccipital; bpt, basipterygoid process; bsp, basisphenoid; bspr, basisphenoid recess; bt, basal tuber; fo, fenestra ovalis; Is, laterosphenoid; oc, occipital condyle; op, opisthotic; pop, paroccipital process; popls, postorbital process of the laterosphenoid; psp, parasphenoid; Roman numbers refer to the foramina for the exits of cranial nerves. Scale bars represent 10 mm.