README

This repository includes collections of modules and scripts for molecular simulation and analysis of condensed-phase systems.

Design Principles

• This repository aims to serve as a bridge between the theoretical formula and production level code.

• It is best to be used as validation of production level code.

• Thus the implementation is a straightforward translation from math as possible, with minimal numerical technicalities. Thus it might not have optimal performance.

• It is light-weight, with minimal dependencies.

Organization

plugins/: external code that may be depended

MDSimple/:

• base/: low-level operations to be used by other modules.

• Each folder is an modules that are mostly independent from others.

scripts:

• wrappers to perform specific end-to-end tasks

Usage

Install in your conda environment.

pip install

Then

import MDSimple

Testing

Most modules and functions are covered by pytest.

Technical Notes

Quantity units

use default units as openmm if not claimed.

nanometers
kilojoules_per_mole
picoseconds

atomic_mass u

kelvin