Supporting Data for "Separation of Flexible Enantiomers in Shear Flow"

This gzipped tar archive contains initial configurations and parameters used for the simulations in the manuscript: "Separation of Flexible Enantiomers in Shear Flow", by Minh Nhat Pham, Levi Cherek, 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 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 analysis or utility file extensions: .hydro : Files containing hydrodynamic properties for a molecular structure, showing computed resistance and diffusion tensors, molecular pitch matrices, and pitch values. .meandisp : Mean displacement of enantiomers in Cartesian coordinates, averaged over initial times and over all enantiomers present in the observation region..lcorr : Orientational correlation function (First-order Legendre correlation function) for all enantiomers inside RNEMD or exchange regions. .gofr : Radial distribution function g(r) for pairs of S-R enantiomers (listed with S_R) and enantiomer-solvent (listed with S_[solvent_name])..dat : Data files containing scalar pitch and moments of pitch values computed from molecular geometries of enantiomers..agr : Grace graphing package data.xyz : XYZ (Cartesian) coordinates for visualization A note on naming conventions. All MD simulations (NVT, NVE, RNEMD) have filenames with a number that signifies simulation replica (1-5). The archive is organized as follows: ./StructOpt/Casodex: Optimization of gas-phase geometries of S- and R-bicalutamide ./StructOpt/SingulairNa: Optimization of gas-phase geometries of S- and R-montelukast sodium ./IncFiles: Files containing molecular definitions to be included with OpenMD's .omd files (atom types, charges, positions) ./ForceFields: GAFF2 force field files (modified for use with OpenMD simulations) ./SingleMol/Casodex: Simulations of one S-bicalutamide molecule in different solvent boxes. ./SingleMol/Casodex/Simulations: Each solvent (SPC/E water, benzene, ethanol, acetone) is a separate sub-directory. Contains equilibration NVT and data-collection NVE simulations. ./SingleMol/Casodex/PitchDistr: Contains a graph of the pitch distributions ./SingleMol/Casodex/PitchData: Contains text files of all computed pitch information (scalar pitch, three moments of pitch) for all sampled geometries of S-bicalutamide in each solvent. Each .dat file comprises all 5 simulation replica (denoted with "5runs"). Also contains .hydro files of S-bicalutamide calculated with each solvent's viscosity. ./SingleMol/SingulairNa: Simulations of one S-montelukast sodium molecule in different solvent boxes. Solvents used are SPC/E water, bezenze, ethanol, and methanol. The directory is organized in a similar manner to ./SingleMol/Casodex/ ./Racemic/Casodex: Simulations of racemic solutions of bicalutamide in acetone. ./Racemic/Casodex/Simulations: Contains equilibration (NVT, NVE) and data-collection RNEMD simulations in corresponding sub-directories. ./Racemic/Casodex/PitchDistr: Contains a graph of the pitch distributions ./Racemic/Casodex/PitchData: Contains text files of all computed pitch information (scalar pitch, three moments of pitch) for all sampled geometries of S-bicalutamide in NVE and RNEMD simulations. Each .dat file comprises all 5 simulation replica (denoted with "5runs"). ./Racemic/Casodex/SeparationData: Contains mean displacement of each chirality and the observation region. Regions of positive z coordinates are denoted with "plus" while regions of negative z coordinates are denoted with "minus". ./Racemic/Casodex/LcorrData: Contains Legendre correlation function of all S and R enantiomer in either the "RNEMD" regions or "exchange" regions. ./Racemic/Casodex/GofrData: Contains radial distribution function g(r) between all atoms of the S-R enantiomer pair ("S_R") or between all atoms of the S-solvent pair ("S_acetone") ./Racemic/SingulairNa: Simulations of racemic solutions of montelukast sodium in ethanol. ./Racemic/Singulair_FA: Simulations of racemic solutions of free acid montelukast in ethanol. The directory is organized in a similar manner to ./Racemic/Casodex/ except for the LcorrData/ and GofrData/ directories as these were not calculated for the free acid simulations. ./Racemic/Singulair_FA/Simulations: Contains equilibration (NVT, NVE) and data-collection RNEMD simulations in corresponding sub-directories. For RNEMD simulations, three different values of momentum flux were imposed, which are categorized by "lowshear", "medshear", and "highshear" sub-directories.