DOI: 10.5281/zenodo.14232346
title: Supporting Data for "Thermal Transport Through CTAB- and MTAB-Functionalized Gold Interfaces using Molecular Dynamics Simulations"

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

"Thermal Transport Through CTAB- and MTAB-Functionalized Gold Interfaces using Molecular Dynamics Simulations", by Sydney A. Shavalier, and J. Daniel Gezelter

A note on naming conventions. All simulations have filenames with with two numbers - one that signifies simulation replica (1-5), and another that signified which step of equilibration/RNEMD was being performed. For example, lowmtab111_3opt4 would signify the third simulation replica of a low coverage MTAB system and a (111) gold facet, which was on its fourth equilibration step after optimization.

The OpenMD simulation engine utilizes 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 sampled 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..rnemd : Contains spatial information about temperatures, densities, etc. for simulations run under reverse non-equilibrium molecular dynamics

Other data analyis or utility file extensions:

 .pack  : Files for creating systems with Packmol .z       : Density \rho(z) for specific selected atom types .r       : Density \rho(r) for specific selected atom types .p2z     : Legendre Polynomial Correlation using z as reference axis .p2r     : Legendre Polynomial Correlation using radial vector as reference axis .chargez : Charge density as a function of z-axis .charger : Charge density as a function of radius .agr     : Grace graphing package data .xyz     : XYZ (Cartesian) coordinates for visualization 

The archive is organized as follows:

  ./CTAB/111: Simulations of Au(111) functionalized with CTAB              final systems begin with "highctab"              RNEMD simulations are in ./CTAB/111/RNEMD  ./CTAB/110: Simulations of Au(110) functionalized with CTAB              final systems begin with "highctab"              RNEMD simulations are in ./CTAB/110/RNEMD  ./CTAB/100: Simulations of Au(100) functionalized with CTAB              final systems begin with "highctab"              RNEMD simulations are in ./CTAB/100/RNEMD  ./MTAB/111: Simulations of Au(111) functionalized with MTAB               final systems begin with "highmtab" or "lowmtab"              RNEMD simulations are in ./MTAB/111/RNEMD  ./MTAB/110: Simulations of Au(110) functionalized with MTAB              final systems begin with "highmtab" or "lowmtab"              RNEMD simulations are in ./MTAB/110/RNEMD  ./MTAB/100: Simulations of Au(100) functionalized with MTAB               final systems begin with "highmtab" or "lowmtab"              RNEMD simulations are in ./MTAB/100/RNEMD  ./MTAB/NP/R10: Simulations of Au Nanoparticles (r = 10 angstroms),              functionalized with MTAB              final systems begin with "highmtab" or "lowmtab"              RNEMD simulations are in ./MTAB/NP/R10/RNEMD

Systems that were run with metal polarizability turned on have 'fq' as part of their filenames.