Create graphene and other substrates for use in molecular dynamics simulations. A binary CLI utility grafen_cli and the library grafen are both available for use.

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_cli [OPTIONS] <PATH>

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

OPTIONS:
    -d, --database <STR>    Path to database
    -t, --title <STR>       Title of output system

ARGS:
    <PATH>    Output GROMOS file

Library

See the documentation for usage examples.

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.

License