DOI: 10.5281/zenodo.18664170
title: Supporting Data for "Elucidating Trace Gas Interactions with Ice Surfaces using Molecular Dynamics"

description: This gzipped tar archive contains initial configurations and parameters used for the simulations in the manuscript:

"Elucidating Trace Gas Interactions with Ice Surfaces using Molecular Dynamics", by Benjamin M. Harless, and J. Daniel Gezelter

OpenMD has a number of file extensions that are present in this archive:

.omd    : A combined MetaData and configuration file that is used to start a simulation .frc    : a force field parameter file.eor    : an 'end of run' or final configuration (same format as .omd).stat   : status file with instantaneous information about energies, temperatures, etc. These are generally large and have not been included, as they can be regenerated easily from the .omd file..report : a post-simulation file containing thermodynamic averages from the .stat file.dump   : a full trajectory file containing positions and velocities ampled at a 'sampleTime' specified in the .omd file. These are generally very large and have not been included, as they can be regenerated from the .omd file.

Other data analyis or utility file extensions:

.pack    : Files for creating systems with Packmol.RhoZ    : Density \rho(z) for specific selected atom types.Qz      : Tetrahedrality q(z) for water molecules.hbg     : Hydrogen bond statistics for selected molecules.OHfreqs : mapped frequencies of OH bonds from local electric fields, projected along the O-H bond vector, using the TIP4P frequency maps of Gruenbaum, et al. ( see doi: 10.1021/ct400292q ).agr     : Grace graphing package data.xyz     : XYZ (Cartesian) coordinates for visualization The archive is organized as follows:

  ./Acetone/223K: Simulations of Basal ice facet with acetone layers @ 223K  ./Acetone/265K: Simulations of Basal ice facet with acetone layers @ 265K  ./Methanol/223K: Simulations of Basal ice facet with methanol layers @ 223K  ./Methanol/265K: Simulations of Basal ice facet with methanol layers @ 265K  ./BareIce/0K: Structures used to obtain ideal OH frequencies from the outer bilayer  ./BareIce/223K: Simulations of a bare Basal ice facet @ 223K  ./BareIce/265K: Simulations of a bare Basal ice facet @ 265K  ./ReferenceFiles: Force field and topology files for use with OpenMD  ./SysConstruct: Packmol and structure files for initial adsorbate layer construction  ./Graphs: All data files used for plotting results in Grace

A note on naming conventions. All MD simulations have filenames with with a number that signifies simulation replica (1-5).

In the lower temperature (223K) directories, filenames starting with  'data' were used for data collection, while other simulation files (often starting with 'NVT') were used for equilibration.

In the higher temperature (265K) directories, data was collected from the last 1 ns of the 5 ns 'NVT' simulations. Also included are simulation files starting with 'warm' (bringing them up to temperature) and 'thermal' (equilibrating at the new temperature). In the 'BareIce/265K' directory, the naming conventions of the low temperature directory was maintained.

The 0K frequency data was collected from molecules at the surface of the Basal_sheet_Vacuum_.omd file in the BareIce/0K directory.