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