cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.35003/blex70/oml9ku
title: Fig7.py

description: :unav
DOI: 10.35003/blex70/qeccho
title: Fig1.py

description: :unav
DOI: 10.35003/blex70/whtazf
title: Fig1_Topography.png

description: :unav
DOI: 10.35003/blex70/zb2ekw
title: Fig4.eps

description: Figure 4
DOI: 10.35003/blex70/42irvo
title: Fig6.eps

description: Figure 6
DOI: 10.35003/blex70/f14kt7
title: Fig7.eps

description: Figure 7
DOI: 10.35003/blex70/jbqrwe
title: Fig4.py

description: Source Code for Figure 4
DOI: 10.35003/blex70/memxod
title: Fig5.eps

description: Figure 5
DOI: 10.35003/blex70/rneg7r
title: Fig8.eps

description: Figure 8
DOI: 10.35003/blex70/0jhxe6
title: Fig9.eps

description: Figure 9
DOI: 10.35003/blex70/jd1utf
title: Fig9.py

description: Source Code for Figure 9
DOI: 10.35003/blex70/jewlgb
title: requirements.txt

description: requirements for python package
DOI: 10.35003/blex70/objlfp
title: Fig8.py

description: Source Code for Figure 8
DOI: 10.35003/blex70/wwix2h
title: main.py

description: main source code to reproduce all figures
DOI: 10.5281/zenodo.10184815
title: MD simulation of POPC bilayer with OPLS3e force field, 1000 mM NaCl part 1

description: MD simulation of POPC (1-palmitoyl-2-oleoyl-phosphatidylcholine) bilayer with OPLS3e force field, 1000 mM NaCl part 1 (0-500ns)

Dataset contains trajectories (_trj) for the first 500ns of the 1000ns trajectory, topology (-out.cms), input files (.cfg, .msj, .cms), and other files.

For the ease of the upload, trajectory files (_trj) are divided to 100ns pieces and tarred (named desmond_md_nacl1000_x-xns.tar.gz)

Dataset also contains Gromacs converted files (.xtc, .gro and .top) 

System: POPC bilayer in water

Number of lipids: 200 (100/leaflet)

Number of waters: 8880

Salt: NaCl

Concentration: 1000 mM

Number of cations: 160

Simulation time: 1000 ns (in this dataset 0-500ns of original trajectories)

Simulation engine: Desmond 2019-4

Temperature: 300 K

Related dataset: MD simulation of POPC bilayer with OPLS3e force field, 1000 mM NaCl part 2

In contrast to previous version, this version contains gromacs format trajectory file .xtc with corrected time steps.
DOI: 10.5281/zenodo.6365066
title: MD simulation of POPC bilayer with OPLS3e force field, 1000 mM NaCl part 1

description: MD simulation of POPC (1-palmitoyl-2-oleoyl-phosphatidylcholine) bilayer with OPLS3e force field, 1000 mM NaCl part 1 (0-500ns)

Dataset contains trajectories (_trj) for the first 500ns of the 1000ns trajectory, topology (-out.cms), input files (.cfg, .msj, .cms), and other files.

For the ease of the upload, trajectory files (_trj) are divided to 100ns pieces and tarred (named desmond_md_nacl1000_x-xns.tar.gz)

Dataset also contains Gromacs converted files (.xtc, .gro and .top) 

System: POPC bilayer in water

Number of lipids: 200 (100/leaflet)

Number of waters: 8880

Salt: NaCl

Concentration: 1000 mM

Number of cations: 160

Simulation time: 1000 ns (in this dataset 0-500ns of original trajectories)

Simulation engine: Desmond 2019-4

Temperature: 300 K

Related dataset: MD simulation of POPC bilayer with OPLS3e force field, 1000 mM NaCl part 2

In contrast to previous version, this version contains gromacs format trajectory file .xtc with corrected time steps.
DOI: 10.5281/zenodo.6365067
title: MD simulation of POPC bilayer with OPLS3e force field, 1000 mM NaCl part 1

description: MD simulation of POPC (1-palmitoyl-2-oleoyl-phosphatidylcholine) bilayer with OPLS3e force field, 1000 mM NaCl part 1 (0-500ns) Dataset contains trajectories (_trj) for the first 500ns of the 1000ns trajectory, topology (-out.cms), input files (.cfg, .msj, .cms), and other files. For the ease of the upload, trajectory files (_trj) are divided to 100ns pieces and tarred (named desmond_md_nacl1000_x-xns.tar.gz) Dataset also contains Gromacs converted files (.xtc, .gro and .top) System: POPC bilayer in water Number of lipids: 200 (100/leaflet) Number of waters: 8880 Salt: NaCl Concentration: 1000 mM Number of cations: 160 Simulation time: 1000 ns (in this dataset 0-500ns of original trajectories) Simulation engine: Desmond 2019-4 Temperature: 300 K Related dataset: MD simulation of POPC bilayer with OPLS3e force field, 1000 mM NaCl part 2
DOI: 10.5281/zenodo.6618809
title: MD simulation of POPC bilayer with OPLS3e force field, 1000 mM NaCl part 1

description: MD simulation of POPC (1-palmitoyl-2-oleoyl-phosphatidylcholine) bilayer with OPLS3e force field, 1000 mM NaCl part 1 (0-500ns) Dataset contains trajectories (_trj) for the first 500ns of the 1000ns trajectory, topology (-out.cms), input files (.cfg, .msj, .cms), and other files. For the ease of the upload, trajectory files (_trj) are divided to 100ns pieces and tarred (named desmond_md_nacl1000_x-xns.tar.gz) Dataset also contains Gromacs converted files (.xtc, .gro and .top) System: POPC bilayer in water Number of lipids: 200 (100/leaflet) Number of waters: 8880 Salt: NaCl Concentration: 1000 mM Number of cations: 160 Simulation time: 1000 ns (in this dataset 0-500ns of original trajectories) Simulation engine: Desmond 2019-4 Temperature: 300 K Related dataset: MD simulation of POPC bilayer with OPLS3e force field, 1000 mM NaCl part 2
DOI: 10.35003/blex70/coampp
title: temperature_3800Myr_L080_C60.txt

description: cold
DOI: 10.35003/blex70/dmyhmq
title: README.md

description: readme
DOI: 10.35003/blex70/dnw9nn
title: Fig1.py

description: Figure 1 - Topographic Map
DOI: 10.35003/blex70/hda5wi
title: temperature_4100Myr_L080_C60.txt

description: intermediate
DOI: 10.35003/blex70/nqlpzh
title: temperature_4400Myr_L080_C60.txt

description: warm
DOI: 10.35003/blex70/havccb
title: Fig4.py

description: Source Code for Figure 4
DOI: 10.35003/blex70/nalr43
title: Fig7.py

description: Source Code for Figures 7a and 7b
DOI: 10.35003/blex70/oqfcpd
title: Fig5_and_6.py

description: Source Code for Figures 5 and 6
DOI: 10.35003/blex70/pkcblh
title: Fig4.eps

description: Figure 4
DOI: 10.35003/blex70/uqhyas
title: Fig3.py

description: Figure 3 - Flexure
DOI: 10.35003/blex70/a1j3ut
title: Fig8.py

description: Source Code for Figure 8
DOI: 10.35003/blex70/dxyo7i
title: lpgrs_high1_elem_abundance_2deg.tab

description: Data File
DOI: 10.35003/blex70/idksvy
title: Fig7.eps

description: Figure 7
DOI: 10.35003/blex70/mjayda
title: Model1_thick.sh

description: Crustal Thickness Data for Figure 7
DOI: 10.35003/blex70/rshcjp
title: Fig9.py

description: Source Code for Figure A1
DOI: 10.35003/blex70/xwiiiz
title: lpgrs_high1_elem_abundance_2deg.lbl

description: Label File
DOI: 10.35003/blex70/15a9mk
title: lpgrs_high1_elem_abundance_2deg.xml

description: Readme, Metadata
DOI: 10.35003/blex70/g78npe
title: lpgrs_elem_abundance_2deg_quicklook.lbl

description: Quicklook
DOI: 10.35003/blex70/gqlx3k
title: lpgrs_high1_elem_abundance_2deg_semicolon.tab

description: Data File for Figure 7b
DOI: 10.35003/blex70/ttowcp
title: lpgrs_elem_abundance_2deg_quicklook.xml

description: Quicklook Metadata
DOI: 10.35003/blex70/wm3svw
title: lpgrs_elem_abundance_2deg_quicklook.pdf

description: Quicklook as pdf
DOI: 10.35003/blex70/4ivcwi
title: README.md

description: readme
DOI: 10.35003/blex70/9ommfi
title: utilis.py

description: :unav
DOI: 10.35003/blex70/buwav4
title: GSA_Plots.py

description: :unav
DOI: 10.35003/blex70/djaftp
title: gray_background_map.txt

description: Alternative Gray Colormap for Figure 7a
DOI: 10.35003/blex70/gn9jcm
title: custom_cmap.py

description: Produce Own Colormaps
DOI: 10.35003/blex70/psinsg
title: constants.py

description: Constants for the python Repository
DOI: 10.35003/blex70/yull40
title: main.py

description: Main source code to reproduce all figures
DOI: 10.5281/zenodo.10534025
title: Changes in Tubular Biomarkers with Dietary Intervention and Metformin in Patients with Autosomal Dominant Polycystic Kidney Disease

description: Data associated with mansucript: Changes in Tubular Biomarkers with Dietary Intervention and Metformin in Patients with Autosomal Dominant Polycystic Kidney Disease
DOI: 10.5281/zenodo.10200685
title: MD simulation of POPC bilayer with OPLS3e force field, 500 mM NaCl part 1

description: MD simulation of POPC (1-palmitoyl-2-oleoyl-phosphatidylcholine) bilayer with OPLS3e force field, 500 mM NaCl part 1 (0-500ns)

Dataset contains trajectories (_trj) for the first 500ns of the 1000ns trajectory, topology (-out.cms), input files (.cfg, .msj, .cms), and other files

For the ease of the upload, trajectory files (_trj) are divided to 100ns pieces and tarred (named desmond_md_nacl500_x-xns.tar.gz)

Dataset also contains Gromacs converted files (.xtc, .gro and .top) 

System: POPC bilayer in water

Number of lipids: 200 (100/leaflet)

Number of waters: 8880

Salt: NaCl

Concentration: 500 mM

Number of cations: 80

Simulation time: 1000 ns (in this dataset 0-500ns of original trajectories)

Simulation engine: Desmond 2019-4

Temperature: 300 K

Related dataset: MD simulation of POPC bilayer with OPLS3e force field, 500 mM NaCl part 2

In contrast to previous version, this version contains gromacs format trajectory file .xtc with corrected time steps.
DOI: 10.5281/zenodo.6364215
title: MD simulation of POPC bilayer with OPLS3e force field, 500 mM NaCl part 1

description: MD simulation of POPC (1-palmitoyl-2-oleoyl-phosphatidylcholine) bilayer with OPLS3e force field, 500 mM NaCl part 1 (0-500ns)

Dataset contains trajectories (_trj) for the first 500ns of the 1000ns trajectory, topology (-out.cms), input files (.cfg, .msj, .cms), and other files

For the ease of the upload, trajectory files (_trj) are divided to 100ns pieces and tarred (named desmond_md_nacl500_x-xns.tar.gz)

Dataset also contains Gromacs converted files (.xtc, .gro and .top) 

System: POPC bilayer in water

Number of lipids: 200 (100/leaflet)

Number of waters: 8880

Salt: NaCl

Concentration: 500 mM

Number of cations: 80

Simulation time: 1000 ns (in this dataset 0-500ns of original trajectories)

Simulation engine: Desmond 2019-4

Temperature: 300 K

Related dataset: MD simulation of POPC bilayer with OPLS3e force field, 500 mM NaCl part 2

In contrast to previous version, this version contains gromacs format trajectory file .xtc with corrected time steps.
DOI: 10.5281/zenodo.6364216
title: MD simulation of POPC bilayer with OPLS3e force field, 500 mM NaCl part 1

description: MD simulation of POPC (1-palmitoyl-2-oleoyl-phosphatidylcholine) bilayer with OPLS3e force field, 500 mM NaCl part 1 (0-500ns) Dataset contains trajectories (_trj) for the first 500ns of the 1000ns trajectory, topology (-out.cms), input files (.cfg, .msj, .cms), and other files For the ease of the upload, trajectory files (_trj) are divided to 100ns pieces and tarred (named desmond_md_nacl500_x-xns.tar.gz) Dataset also contains Gromacs converted files (.xtc, .gro and .top) System: POPC bilayer in water Number of lipids: 200 (100/leaflet) Number of waters: 8880 Salt: NaCl Concentration: 500 mM Number of cations: 80 Simulation time: 1000 ns (in this dataset 0-500ns of original trajectories) Simulation engine: Desmond 2019-4 Temperature: 300 K Related dataset: MD simulation of POPC bilayer with OPLS3e force field, 500 mM NaCl part 2
DOI: 10.5281/zenodo.6618810
title: MD simulation of POPC bilayer with OPLS3e force field, 500 mM NaCl part 1

description: MD simulation of POPC (1-palmitoyl-2-oleoyl-phosphatidylcholine) bilayer with OPLS3e force field, 500 mM NaCl part 1 (0-500ns) Dataset contains trajectories (_trj) for the first 500ns of the 1000ns trajectory, topology (-out.cms), input files (.cfg, .msj, .cms), and other files For the ease of the upload, trajectory files (_trj) are divided to 100ns pieces and tarred (named desmond_md_nacl500_x-xns.tar.gz) Dataset also contains Gromacs converted files (.xtc, .gro and .top) System: POPC bilayer in water Number of lipids: 200 (100/leaflet) Number of waters: 8880 Salt: NaCl Concentration: 500 mM Number of cations: 80 Simulation time: 1000 ns (in this dataset 0-500ns of original trajectories) Simulation engine: Desmond 2019-4 Temperature: 300 K Related dataset: MD simulation of POPC bilayer with OPLS3e force field, 500 mM NaCl part 2
DOI: 10.5066/p9u9i10s
title: Compilation of total organic carbon and pyrolysis analysis data for Cretaceous marine shales in the Raton Basin-Sierra Grande Uplift Province, Colorado and New Mexico

description: This compilation presents total organic carbon and pyrolysis analysis data for the Pierre Shale, Niobrara Formation, and other Cretaceous marine shales in the Raton Basin-Sierra Grande Uplift Province. The data was used to characterize these potential source rock intervals in support of the oil and gas resource assessment in the province. The data was compiled from the publicly available files at the USGS Core Research Center in Lakewood, Colorado and from published literature.
DOI: 10.5281/zenodo.6361725
title: MD simulation of POPC bilayer with OPLS3e force field, 200 mM NaCl part 1

description: MD simulation of POPC bilayer with OPLS3e force field, 200 mM NaCl part 1 Dataset contains trajectories (_trj) for the first 500ns of the 1000ns trajectory, topology (-out.cms) and input files (.cfg, .msj, .cms), and other files For the ease of the upload, trajectory files (_trj) are divided to 100ns pieces and tarred (named desmond_md_nacl200_x-xns.tar.gz) Dataset also contains Gromacs converted files (.xtc, .gro and .top). Converted trajectory is also for the first 500 ns of 1000 ns trajectory System: POPC bilayer in water Number of lipids: 200 (100/leaflet) Number of waters: 8880 Concentration: 200 mM Number of cations: 32 Simulation time: 1000 ns (in this dataset 0-500ns) Simulation engine: Desmond 2019-4 Temperature: 300 K Related dataset: MD simulation of POPC bilayer with OPLS3e force field, 200 mM NaCl part 2
DOI: 10.5281/zenodo.6618822
title: MD simulation of POPC bilayer with OPLS3e force field, 200 mM NaCl part 1

description: MD simulation of POPC bilayer with OPLS3e force field, 200 mM NaCl part 1 Dataset contains trajectories (_trj) for the first 500ns of the 1000ns trajectory, topology (-out.cms) and input files (.cfg, .msj, .cms), and other files For the ease of the upload, trajectory files (_trj) are divided to 100ns pieces and tarred (named desmond_md_nacl200_x-xns.tar.gz) Dataset also contains Gromacs converted files (.xtc, .gro and .top). Converted trajectory is also for the first 500 ns of 1000 ns trajectory System: POPC bilayer in water Number of lipids: 200 (100/leaflet) Number of waters: 8880 Concentration: 200 mM Number of cations: 32 Simulation time: 1000 ns (in this dataset 0-500ns) Simulation engine: Desmond 2019-4 Temperature: 300 K Related dataset: MD simulation of POPC bilayer with OPLS3e force field, 200 mM NaCl part 2
DOI: 10.5281/zenodo.10202795
title: MD simulation of POPC bilayer with OPLS3e force field, 200 mM NaCl part 1

description: MD simulation of POPC bilayer with OPLS3e force field, 200 mM NaCl part 1

Dataset contains trajectories (_trj) for the first 500ns of the 1000ns trajectory, topology (-out.cms) and input files (.cfg, .msj, .cms), and other files

For the ease of the upload, trajectory files (_trj) are divided to 100ns pieces and tarred (named desmond_md_nacl200_x-xns.tar.gz)

Dataset also contains Gromacs converted files (.xtc, .gro and .top). Converted trajectory is also for the first 500 ns of 1000 ns trajectory

System: POPC bilayer in water

Number of lipids: 200 (100/leaflet)

Number of waters: 8880

Concentration: 200 mM

Number of cations: 32

Simulation time: 1000 ns (in this dataset 0-500ns)

Simulation engine: Desmond 2019-4

Temperature: 300 K

Related dataset: MD simulation of POPC bilayer with OPLS3e force field, 200 mM NaCl part 2

In contrast to previous version, this version contains gromacs format trajectory file .xtc with corrected time steps.
DOI: 10.5281/zenodo.6361724
title: MD simulation of POPC bilayer with OPLS3e force field, 200 mM NaCl part 1

description: MD simulation of POPC bilayer with OPLS3e force field, 200 mM NaCl part 1

Dataset contains trajectories (_trj) for the first 500ns of the 1000ns trajectory, topology (-out.cms) and input files (.cfg, .msj, .cms), and other files

For the ease of the upload, trajectory files (_trj) are divided to 100ns pieces and tarred (named desmond_md_nacl200_x-xns.tar.gz)

Dataset also contains Gromacs converted files (.xtc, .gro and .top). Converted trajectory is also for the first 500 ns of 1000 ns trajectory

System: POPC bilayer in water

Number of lipids: 200 (100/leaflet)

Number of waters: 8880

Concentration: 200 mM

Number of cations: 32

Simulation time: 1000 ns (in this dataset 0-500ns)

Simulation engine: Desmond 2019-4

Temperature: 300 K

Related dataset: MD simulation of POPC bilayer with OPLS3e force field, 200 mM NaCl part 2

In contrast to previous version, this version contains gromacs format trajectory file .xtc with corrected time steps.
DOI: 10.6084/m9.figshare.24056673
title: Plant-plant communication in <i>Camellia japonica</i> and <i>Camellia rusticana</i> via volatiles

description: Experiments 1 was conducted to explore if Camellia species response to damaged plant volatiles. Intact branches of damaged plant (intra-plant) or neighboring plant (inter-plant) were exposed to artificially damaged plant volatiles (ADPVs) and measured the proportion of damage one month later.Experiments 2 was conducted to confirm that Camellia’s volatiles include cues to induce resistance. Air was transferred from head space of damaged leaves to that of intact leaves. Air-injected leaves were measured the accumulation of damage during 3 months after treatment.
DOI: 10.6084/m9.figshare.24056673.v2
title: Plant-plant communication in <i>Camellia japonica</i> and <i>Camellia rusticana</i> via volatiles

description: Experiments 1 was conducted to explore if Camellia species response to damaged plant volatiles. Intact branches of damaged plant (intra-plant) or neighboring plant (inter-plant) were exposed to artificially damaged plant volatiles (ADPVs) and measured the proportion of damage one month later.Experiments 2 was conducted to confirm that Camellia’s volatiles include cues to induce resistance. Air was transferred from head space of damaged leaves to that of intact leaves. Air-injected leaves were measured the accumulation of damage during 3 months after treatment.
DOI: 10.6084/m9.figshare.24056673.v1
title: Plant-plant communication in <i>Camellia japonica</i> and <i>Camellia rusticana</i> via volatiles

description: Experiments 1 was conducted to explore if Camellia species response to damaged plant volatiles. Intact branches of damaged plant (intra-plant) or neighboring plant (inter-plant) were exposed to artificially damaged plant volatiles (ADPVs) and measured the proportion of damage one month later.Experiments 2 was conducted to confirm that Camellia’s volatiles include cues to induce resistance. Air was transferred from head space of damaged leaves to that of intact leaves. Air-injected leaves were measured the accumulation of damage during 3 months after treatment.
DOI: 10.5281/zenodo.10203643
title: MD simulation of POPC bilayer with OPLS3e force field, 100 mM NaCl part 1

description: MD simulation of POPC bilayer with OPLS3e force field, 100 mM NaCl part 1 (0-500ns)

Dataset contains trajectories (_trj) for the first 500ns of the 1000ns trajectory, topologies (-out.cms), input files (.cfg, .msj, .cms) and other files.

For the ease of the upload, trajectory files (_trj) are divided to 100ns pieces and tarred (named desmond_md_nacl100_x-xns.tar.gz).

Dataset also contains Gromacs converted files (.xtc, .gro and .top). Converted trajectory is also for the first 500 ns of 1000 ns trajectory

System: POPC bilayer in water

Number of lipids: 200 (100/leaflet)

Number of waters: 8880

Concentration: 100 mM

Number of cations: 16

Simulation time: 1000 ns (in this dataset 0-500ns)

Simulation engine: Desmond 2019-4

Temperature: 300 K

Related dataset: MD simulation of POPC bilayer with OPLS3e force field, 100 mM NaCl part 2

In contrast to previous version, this version contains gromacs format trajectory file .xtc with corrected time steps.
DOI: 10.5281/zenodo.6355374
title: MD simulation of POPC bilayer with OPLS3e force field, 100 mM NaCl part 1

description: MD simulation of POPC bilayer with OPLS3e force field, 100 mM NaCl part 1 (0-500ns)

Dataset contains trajectories (_trj) for the first 500ns of the 1000ns trajectory, topologies (-out.cms), input files (.cfg, .msj, .cms) and other files.

For the ease of the upload, trajectory files (_trj) are divided to 100ns pieces and tarred (named desmond_md_nacl100_x-xns.tar.gz).

Dataset also contains Gromacs converted files (.xtc, .gro and .top). Converted trajectory is also for the first 500 ns of 1000 ns trajectory

System: POPC bilayer in water

Number of lipids: 200 (100/leaflet)

Number of waters: 8880

Concentration: 100 mM

Number of cations: 16

Simulation time: 1000 ns (in this dataset 0-500ns)

Simulation engine: Desmond 2019-4

Temperature: 300 K

Related dataset: MD simulation of POPC bilayer with OPLS3e force field, 100 mM NaCl part 2

In contrast to previous version, this version contains gromacs format trajectory file .xtc with corrected time steps.
DOI: 10.5281/zenodo.6355375
title: MD simulation of POPC bilayer with OPLS3e force field, 100 mM NaCl part 1

description: MD simulation of POPC bilayer with OPLS3e force field, 100 mM NaCl part 1 (0-500ns) Dataset contains trajectories (_trj) for the first 500ns of the 1000ns trajectory, topologies (-out.cms), input files (.cfg, .msj, .cms) and other files. For the ease of the upload, trajectory files (_trj) are divided to 100ns pieces and tarred (named desmond_md_nacl100_x-xns.tar.gz). Dataset also contains Gromacs converted files (.xtc, .gro and .top). Converted trajectory is also for the first 500 ns of 1000 ns trajectory System: POPC bilayer in water Number of lipids: 200 (100/leaflet) Number of waters: 8880 Concentration: 100 mM Number of cations: 16 Simulation time: 1000 ns (in this dataset 0-500ns) Simulation engine: Desmond 2019-4 Temperature: 300 K Related dataset: MD simulation of POPC bilayer with OPLS3e force field, 100 mM NaCl part 2
DOI: 10.5281/zenodo.6619578
title: MD simulation of POPC bilayer with OPLS3e force field, 100 mM NaCl part 1

description: MD simulation of POPC bilayer with OPLS3e force field, 100 mM NaCl part 1 (0-500ns) Dataset contains trajectories (_trj) for the first 500ns of the 1000ns trajectory, topologies (-out.cms), input files (.cfg, .msj, .cms) and other files. For the ease of the upload, trajectory files (_trj) are divided to 100ns pieces and tarred (named desmond_md_nacl100_x-xns.tar.gz). Dataset also contains Gromacs converted files (.xtc, .gro and .top). Converted trajectory is also for the first 500 ns of 1000 ns trajectory System: POPC bilayer in water Number of lipids: 200 (100/leaflet) Number of waters: 8880 Concentration: 100 mM Number of cations: 16 Simulation time: 1000 ns (in this dataset 0-500ns) Simulation engine: Desmond 2019-4 Temperature: 300 K Related dataset: MD simulation of POPC bilayer with OPLS3e force field, 100 mM NaCl part 2
DOI: 10.18746/bmth.data.00000329
title: Tool and Codes for Simulator-based-Digital-Twin
DOI: 10.5281/zenodo.10212566
title: MD simulation of POPC bilayer with OPLS3e force field, 50 mM CaCl2 part 1

description: MD simulation of POPC bilayer with OPLS3e force field, 50 mM CaCl2 part 1 (0-500ns)

Dataset contains trajectories (_trj) for the first 500ns of the 1000ns trajectory, topology (-out.cms), input files (.cfg, .msj, .cms), and other files.

For the ease of the upload, trajectory files (_trj) are divided to 100ns pieces and tarred (named desmond_md_cacl50_x-xns.tar.gz)

Dataset also contains Gromacs converted files (.xtc, .gro and .top). Converted trajectory contains equilibrated piece of the trajectory (500-1000ns)

System: POPC bilayer in water

Number of lipids: 200 (100/leaflet)

Number of waters: 8880

Salt: CaCl2

Concentration: 50 mM

Number of cations: 8

Simulation time: 1000 ns (in this dataset 0-500ns)

Simulation engine: Desmond 2019-4

Temperature: 300 K

Related dataset: MD simulation of POPC bilayer with OPLS3e force field, 50 mM CaCl2 part 2

In contrast to previous version, this version contains gromacs format trajectory file .xtc with corrected time steps.