MolSimToolkit.jl

MolSimToolkit.jl is a Julia package for analyzing molecular dynamics (MD) simulations. It provides fast, flexible tools for trajectory analysis, structural alignment, secondary structure mapping, and more. The toolkit is designed to be lightweight and extensible, making it easy to build custom analysis workflows.

Features

• Robust structural alignment (MDLovoFit)
• Secondary structure mapping and plotting helpers
• Hydrogen bond analysis
• Pairwise and molecular distance analysis / coordination numbers
• Utilities for system setup (integrated with Packmol)
• Block averaging and replica exchange analysis
• Integration with PDBTools.jl

Installation

Install via Julia's package manager:

import Pkg
Pkg.add("MolSimToolkit")

It is recommended to also install PDBTools for enhanced functionality:

Pkg.add("PDBTools")

Quick Start

using MolSimToolkit

Example: Robust Alignment (MDLovoFit)

using MolSimToolkit, MolSimToolkit.Testing
sim = Simulation(Testing.mdlovofit_pdb, Testing.mdlovofit_traj)
fractions = map_fractions(sim)                # Scan fractions and RMSDs
aligned = mdlovofit(sim; fraction=0.8)        # Align trajectory using 80% least-mobile atoms

Example: Secondary Structure Map

using MolSimToolkit, MolSimToolkit.Testing
sim = Simulation(Testing.namd_pdb, Testing.namd_traj)
ssmap = ss_map(sim; selection="residue >= 30 and residue <= 35")
hcontent = ss_mean(ssmap; class="H")

Example: Hydrogen Bonds

using MolSimToolkit, PDBTools
sim = Simulation(Testing.namd_pdb, Testing.namd_traj)
hbs = hydrogen_bonds(sim, "protein" => "water")

Example: Molecular Minimum Distances

using MolSimToolkit
list = MolSimToolkit.MolecularMinimumDistances.minimum_distances(
        xpositions=water, 
        ypositions=protein, 
        xn_atoms_per_molecule=3, 
        cutoff=12.0, 
        unitcell=[83.115,83.044,83.063]
)

Documentation

• Stable Docs
• Dev Docs

Contributing

Contributions are welcome! Please open issues or pull requests.

License

MIT License. See LICENSE for details.