mupt-examples

Installation

To obtain a copy of these examples, clone this repo and navigate into it, via:

git clone https://github.com/MuPT-hub/mupt-examples # this repo
cd mupt-examples

Create the demo environment and start JupyterLab with Mamba:

mamba env create -f conda-envs/mupt-demo-env.yml
mamba activate mupt-demo-env
jupyter lab

The environment installs the supported MuPT release and the dependencies required by the demo notebooks.

Index of examples

End-to-End workflow examples (quickstart):

1. Building a dense polymer melt Allows a user to provide various monomer SMILES, DOP, statistical distribution of monomers, and a density to construct initial coordinates for a dense polymer melt.
2. Simulate the melt Showcases how one can take the system constructed in notebook 1 and assign force field parameters via OpenFF Interchange, export to OpenMM|GROMACS|LAMMPS, and demo a short OpenMM simulation, with optional analysis via MDAnalysis.

System building examples (high-level):

0. Simple peptide example
   Assembles a MuPT representation component hierarchy for a peptide generated from your choice of FASTA string
   Depicts the topological and hierarchical organization of parts in a colorful graphic with 2D coordinates
1. Backmapped chain/melt building
   Shows how to perform a backmapping-like build procedure to go from nothing to an MD starting structure using MuPT tools
   Allows specification of arbitrary homopolymer or copolymer chemistry, number of chains, and distribution of chain length
2. Parameterization, export, and MD simulations with OpenFF
   Shows how to use the OpenFF toolkit to parameterize and export MD input files from a MuPT-build starting structure (obtained from the previous demo)
   Concludes by running a short MD simulation in OpenMM

MuPT Representation components tutorials (low-level):

0. "Molecule from scratch" - bare basics
   Shows how to initialize a basic "bond graph" hierarchy with no coordinates
1. "Molecule from scratch" - advanced usage
   "Kitchen sink" tutorial of how to build a molecule fragment with complete hierarchical info using nothing but MuPT representation components
   Generates physically-plausible coordinates and topology using no force fields or external coordinate embedding algorithms (just basic knowledge of point groups)
   and shows how one can leverage the concurrent, arbitrary resolutions structure of the representation to organize initialization around chemically-meaningful motifs
2. Molecule from SMILES/RDKit
   Shows how to instantiate MuPT representation hierarchies from RDKit Mols and SMILES string
3. Rigid body shapes
   Shows off that different kinds of shapes that MuPT Primitive objects can take on (PointClouds, Spheres, Ellipsoids, and Rods)
4. Inter-body spatial alignment Generates animated trajectories which illustrate the different kinds of inter-body alignment operations MuPT uses to spatially align all MuPT representation components