title: Simulation Files for Organic Contaminants and Atmospheric Nitrogen at the Graphene–Water Interface
author: Thakkar, Ravindra
description: This data set provides files needed to run the simulations described in the manuscript entitled "Organic contaminants and atmospheric nitrogen at the graphene–water interface: A simulation study" using the molecular dynamics software NAMD and LAMMPS. The output of the simulations, as well as scripts used to analyze this output, are also included. The files are organized into directories corresponding to the figures of the main text and supplementary information. They include molecular model structure files (NAMD psf), force field parameter files (in CHARMM format), initial atomic coordinates (pdb format), NAMD or LAMMPS configuration files, Colvars configuration files, NAMD log files, and NAMD output including restart files (in binary NAMD format) and some trajectories in dcd format (downsampled). Analysis is controlled by shell scripts (Bash-compatible) that call VMD Tcl scripts. A modified LAMMPS C++ source file is also included.