syn2018 / genmd

generation scripts for molecular dynamics initial conditions

This is a package to generate a variety of systems of nanoparticle for use in HOOMD simulations

An example of creating a Binary system of DNA grafted Spherical Nanoparticles run

$ cd examples
$ python run.py 

This will create a simulation folder. If you have HOOMD installed, go inside and run

HOOMD rigid_dna.hoomd

This particular set up will self assemble into a bcc crystal lattice

Note this package is in the process of being refactored and so currently many files have syntax errors

and incorrect paths.

For developers

builders

build systems of nanoparticles, these are good examples to look at for building complex systems

shapes

These are nanoparticle shapes that can be used by builders to create systems of different particles

augmenters

These are objects that can be attached to shapes, currently only DNA

utils

Contains many useful functions for building nanoparticles

Examples

contains and example of run.py which will create a simulation for HOOMD

author: Chris Knorowski contact: [email protected]