Condensed-phase molecular representation to link structure and thermodynamics in molecular dynamics

Code accompanying the publication at https://doi.org/10.1021/acs.jctc.3c00201

The scripts were created specifically for this project, with specific expectations for directory paths and some hard-coded filenames and other settings.

Python version >= 3.9
package list requirements.txt

Inserting angles and constraints into the GROMACS topology files for small molecule graphs:

isomorphism_find_unique.py
- A small number of structures make up the entire set, the variations between the small molecules are based on different combinations of coarse-grained bead types.
make_template_file.py
- Suitable angles and constraints are manually optimized for one example of each of the recurring structures and subsequently used as a template.
isomorphs_insert_constraints.py
- Iterating over the entire set of small molecule graphs, identifiying the correct template and inserting the settings for angles and constraints.

Generating the SLATM representations:

The Spectrum of London and Axilrod-Teller-Muto (SLATM) potential was defined by Huang, Symonds and von Lilienfeld, https://arxiv.org/abs/1807.04259.

analyze_structures.py
- Handles loading of trajectory files and the required steps to translate the coarse-grained MD trajectories into SLATM representations.
- clean_trajectories.py
  - Corrects for periodic boundary conditions, centers systems around the solutes, selects frames by solute position.
- preprocessing.py
  - Selects solutes and environment particles within the long-range interaction cutoff distance around the solutes' center of mass.
- generate_representations.py
  - Handles the generation of the list of possible many-body interactions and unique particle identifiers required by the QML SLATM method.
  - Generates the SLATM representations.
  - Saves the results as pickled pandas dataframes.

Analyzing a set of SLATM representations with PCA:

analyze_SLATMs.py
- Loads the SLATM representations and required additional files,
- Handles preprocessing of SLATM representations including normalization for PCA
- PCA embedding of the SLATM representations

Visualizing the PCA results: