Dataset Open Access

# Vertical Compositional Variations of liquid hydrocarbons in Titan's Alkanofers

Cordier, Daniel; Bonhommeau, David A.; Tuan, H. Vu; Choukroun, Mathieu; Garcia-Sanchez, Fernando

### Citation Style Language JSON Export

{
"publisher": "Zenodo",
"DOI": "10.5281/zenodo.4975047",
"language": "eng",
"title": "Vertical Compositional Variations of liquid hydrocarbons in Titan's Alkanofers",
"issued": {
"date-parts": [
[
2021,
6,
17
]
]
},
"abstract": "<p>This data set is composed of six archives (.TAR) which collect input and output files from GROMACS (2018 version) simulations on binary and ternary mixtures representative of liquids in Titan&#39;s alkanofers:<br>\n3000CH4+1000C2H6+1000N2_90K.tar<br>\n3000CH4+1000C2H6+1000N2_95K.tar<br>\n4000CH4+1000C2H6_90K.tar<br>\n4000CH4+1000C2H6_95K.tar<br>\n4000CH4+1000N2_90K.tar<br>\n4000CH4+1000N2_95K.tar</p>\n\n<p>The system under study is always composed of 5000 molecules. Simulations at 90 K correspond to a pressure of 1.5 bar while those at 95K correspond to a pressure of 120 bar.</p>\n\n<p>Each archive contains 5 directories:</p>\n\n<p>1)<strong> INPUTS:</strong> It contains all the GROMACS input files (.GRO, .ITP, .TOP) needed to build the simulation box as well as the files required to prepare the molecular dynamics (MD) simulations (.MDP and .TPR). More details about the content of these files is available in the GROMACS manual (https://www.gromacs.org/).<br>\n2 README files are added to inform the reader on useful GROMACS commands used here:<br>\n- README_box.txt: commands to build the simulation box.<br>\n- README_NVT+NPT-runs.dat: commands to run MD simulations and treat some data.</p>\n\n<p>2) <strong>NVTOUT_EQ</strong>: It contains all the files related to the 1-ns NVT equilibration phase, namely, the script for job submission (.SH) together with the related standard ouput files (.OUT and .ERR), and typical GROMACS output files (.GRO, .LOG, .EDR, .TRR, .CPT).<br>\nPost-treatment data are collected in 2 files:<br>\n- stats_nvt-eq.dat: Average potential energy, kinetic energy, total energy, temperature and pressure.<br>\n- energy_nvt-eq.xvg: Potential energy (col. 2), kinetic energy (col. 3), total energy (col. 4), temperature (col. 5), and pressure (col. 6) as a function of time (col.1).</p>\n\n<p>3) <strong>NPTOUT_EQ</strong>: It contains the same kind of files as NVTOUT_EQ but for the first 9 ns of the 19-ns NPT equilibration phase.<br>\nPost-treatment data are collected in 2 files:<br>\n- stats_npt-eq.dat: Average potential energy, kinetic energy, total energy, temperature, pressure, volume, density, and enthalpy.<br>\n- energy_npt-eq.xvg: Potential energy (col. 2), kinetic energy (col. 3), total energy (col. 4), temperature (col. 5),&nbsp; and pressure (col. 6), volume (col.7), density (col.8), and enthalpy (col. 9) as a function of time (col. 1).</p>\n\n<p>4) <strong>NPTOUT_EQ-RERUN1</strong>: It contains the same kind of files as NPTOUT_EQ but for the last 10 ns of the 19-ns NPT equilibration phase.</p>\n\n<p>5) <strong>NPTOUT_ACC</strong>: It contains the same kind of files as NPTOUT_EQ but for the 10-ns NPT accumulation phase. Additional data files also provide diffusion coefficients and shear viscosities depending on the mixture under consideration (see below).</p>\n\n<p><em>For binary mixtures</em>, the mean squared displacements (MSD) of species and the corresponding diffusion coefficients are estimated with the &quot;gmx msd&quot; GROMACS command.<br>\nData are collected in two files:<br>\n- msd-CH4.xvg / msd-C2H6.xvg / msd-N2.xvg: MSD (col. 2) as a function of time (col. 1).&nbsp; The value of the corresponding diffusion coefficient (in cm<sup>2 </sup>s<sup>-1</sup>) is indicated as a comment in the preamble of these files.<br>\n- DCH4.dat / DC2H6.dat / DN2.dat: Estimated diffusion coefficient (in cm<sup>2 </sup>s<sup>-1</sup>) for the three moelcules under study.</p>\n\n<p><em>For ternary mixtures</em>, transverse current autocorrelation functions (TCAF) are computed with the &quot;gmx tcaf&quot; GROMACS command to get values of the shear viscosity:<br>\n- tcaf-slurm.sh, tcaf.out tcaf.xvg. tcaf_all.xvg, tcaf_cub.xvg, tcaf_fit.xvg: script (.SH) and several output files with transverse current autocorrelation functions (.XVG).<br>\n- visc_k.xvg: shear viscosity (col.2) as a function of the wave number (col.1). The last four viscosities can be fitted to get the shear viscosity at infinite wavelength (see GROMACS manual).</p>",
"author": [
{
"family": "Cordier, Daniel"
},
{
"family": "Bonhommeau, David A."
},
{
"family": "Tuan, H. Vu"
},
{
"family": "Choukroun, Mathieu"
},
{
"family": "Garcia-Sanchez, Fernando"
}
],
"note": "Data on larger systems composed of 50 000 molecules are available upon request from the authors.",
"version": "1.0.0",
"type": "dataset",
"id": "4975047"
}
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