Create graphene and other substrates for use in molecular dynamics simulations.

This is a pet project to help me set up simulation systems for my research. It is focused on formats used by Gromacs.

Usage

USAGE:
    grafen [OPTIONS]

FLAGS:
    -h, --help       Prints help information
    -V, --version    Prints version information

OPTIONS:
    -d, --database <PATH>    Path to database
    -o, --output <PATH>      Output GROMOS configuration file (conf.gro)
    -t, --title <STR>        Title of output system

Available Substrates

Substrate definitions are read from a JSON database. An example is provided in include/database.json. This database contains a few residue and the following substrate definitions:

Graphene

A monolayer of carbon atoms set in a hexagonal honeycomb structure. The spacing between every atom is 0.142 nm.

Silica

A monolayer of rigid SiO2 molecules set in a triclinic formation with with spacing 0.450 nm along both base vectors and an angle of 60 degrees between them.

Development

See the documentation.

License

The program is unlicensed. See unlicense.org for details.