Molecular Dynamics

A Python and Rust library for molecular dynamics. Compatible with Linux, Windows, and Mac. Uses CPU with threadpools and SIMD, or an Nvidia GPU.

Warning: Very early release! Lots of missing features. If you see something, post a Github issue.

It uses traditional forcefield-based molecular dynamics, and is inspired by Amber. It does not use quantum-mechanics, nor ab-initio methods.

It uses the Bio-Files dependency to load molecule and force-field files.

Please reference the API documentation for details on the functionality of each data structure and function. You may with to reference the Bio Files API docs as well.

Note: The Python version is CPU-only for now Note: We currently only support saving and loading snapshots/trajectories in a custom format.

Goals

• Runs traditional MD algorithms accurately

• Easy to install, learn, and use

• Fast

• Easy integration into workflows, scripting, and applications

Installation

Python: pip install mol_dynamics biology_files

Rust: Ad dynamics to Cargo.toml

For a GUI application that uses this library, download the Daedalus molecule viewer This provides an easy-to-use way to set up the simulation, and play back trajectories.

Parameters

Integrates the following Amber parameters:

• Small organic molecules, e.g. ligands: General Amber Force Fields: GAFF2

• Protein and amino acids: FF19SB

• Nucleic acids: Amber OL3 and RNA libraries

• Lipids: lipids21

• Carbohydrates: GLYCAM_06j

• Water: Explicit, with OPC

The algorithm

This library uses a traditional MD workflow. We use the following components:

Integrators, and thermostats/barostats

We provide a Velocity-Verlet integrator. It can be used with a Berendsen barostat, and either a CSVR/Bussi, or Langevin thermostat (Middle or traditional). These continuously update atom velocities (for molecules and solvents) to match target pressure and temperatures. The Langevin Middle thermostat is a good starting point.

Solvation

We use an explicit water solvation model: A 4-point rigid OPC model, with a point partial charge on each Hydrogen, and a M (or EP) point offset from the Oxygen. We use the SETTLE algorithm to maintain rigidity, while applying forces to each atom. Only the Oxygen atom carries a Lennard Jones(LJ) force.

Bonded forces

We use Amber-style spring-based forces to maintain covalent bonds. We maintain the following parameters:

• Bond length between each covalently-bonded atom pair

• Angle (sometimes called valence angle) between each 3-atom line of covalently-bonded atoms. (4atoms, 2 bonds)

• Dihedral (aka torsion) angles between each 4-atom line of covalently-bonded atoms. (4 atoms, 3 bonds). These usually have rotational symmetry of 2 or 3 values which are stable.

• Improper Dihedral angles between 4-atoms in a hub-and-spoke configuration. These, for example, maintain stability

• where rings meet other parts of the molecule, or other rings.

Non-bonded forces

These are Coulomb and Lennard Jones (LJ) interactions. These make up the large majority of computational effort. Coulomb forces represent electric forces occurring from dipoles and similar effects, or ions. We use atom-centered pre-computed partial charges for these. They occur within a molecule, between molecules, and between molecules and solvents.

We use a neighbors list (Sometimes called Verlet neighbors; not directly related to the Verlet integrator) to reduce computational effort. We use the SPME Ewald approximation to reduce computation time. This algorithm is suited for periodic boundary conditions, which we use for the solvent.

We use Amber's scaling and exclusion rules: LJ and Coulomb force is reduced between atoms separated by 1 and 2 covalent bonds, and skipped between atoms separated by 3 covalent bonds.

We have two modes of handling Hydrogen in bonded forces: The same as other atoms, and rigid, with position maintained using SHAKE and RATTLE algorithms. The latter allows for stability under higher timesteps. (e.g. 2ps)

Initial relaxation

We run a relaxation / energy-minimization function prior to starting each simulation. This adjusts atom positions to reduce the amount of energy that comes from initial conditions deviating from bonded parameters.

Floating point precision

Mixed precision: 32-bit floating points for most operations. We use 64-bit accumulators, and in thermostat and barostat computations.

Saving results

Snapshots of results can be returned in memory, or saved to disk in DCD format.

More info

We plan to support carbohydrates and lipids later. If you're interested in these, please add a Github Issue.

These general parameters do not need to be loaded externally; they provide the information needed to perform MD with any amino acid sequence, and provide a baseline for dynamics of small organic molecules. You may wish to load frcmod data over these that have overrides for specific small molecules.

This program can automatically load ligands with Amber parameters, for the Amber Geostd set. This includes many common small organic molecules with force field parameters, and partial charges included. It can infer these from the protein loaded, or be queried by identifier.

You can load these molecules with parameters directly from the GUI by typing the identifier. If you load an SDF molecule, the program may be able to automatically update it using Amber parameters and partial charges.

For details on how dynamics using this parameterized approach works, see the Amber Reference Manual. Section 3 and 15 are of particular interest, regarding force field parameters.

Molecule-specific overrides to these general parameters can be loaded from .frcmod and .dat files. We delegate this to the bio files library.

We load partial charges for ligands from mol2, PDBQT etc files. Protein dynamics and water can be simulated using parameters built-in to the program (The Amber one above). Simulating ligands requires the loaded file (e.g. mol2) include partial charges. we recommend including ligand-specific override files as well, e.g. to load dihedral angles from .frcmod that aren't present in Gaff2.

Example use (Python):

from biology_files import Mol2, MmCif, ForceFieldParams
from mol_dynamics import *


def setup_dynamics(mol: Mol2, protein: MmCif, param_set: FfParamSet, lig_specific: ForceFieldParams) -> MdState:
    """
    Set up dynamics between a small molecule we treat with full dynamics, and a rigid one 
    which acts on the system, but doesn't move.
    """

    mols = [
        MolDynamics(
            ff_mol_type=FfMolType.SmallOrganic,
            atoms=mol.atoms,
            # Pass a [Vec3] of starting atom positions. If absent,
            # will use the positions stored in atoms.
            atom_posits=None,
            bonds=mol.bonds,
            # Pass your own from cache if you want, or it will build.
            adjacency_list=None,
            static_=False,
            # This is usually mandatory for small organic molecules. Provided, for example,
            # in Amber FRCMOD files. Overrides general params.
            mol_specific_params=lig_specific,
        ),
        MolDynamics(
            ff_mol_type=FfMolType.Peptide,
            atoms=protein.atoms,
            atom_posits=None,
            bonds=[],  # Not required if static.
            adjacency_list=None,
            static_=True,
            mol_specific_params=None,
        ),
    ]

    return MdState(
        MdConfig(),
        mols,
        param_set,
    )


def main():
    mol = Mol2.load("CPB.mol2")
    protein = MmCif.load("1c8k.cif")

    param_set = FfParamSet.new_amber()
    lig_specific = ForceFieldParams.load_frcmod("CPB.frcmod")
    
    # Add Hydrogens, force field type, and partial charge to atoms in the protein; these usually aren't
    # included from RSCB PDB. You can also call `populate_hydrogens_dihedrals()`, and
    # `populdate_peptide_ff_and_q() separately.
    prepare_peptide(
        protein.atoms,
        protein.residues,
        protein.chains,
        param_set.peptide_ff_q_map,
        7.0,
    )
    
    md = setup_dynamics(mol, protein, param_set, lig_specific)
    
    n_steps = 100
    dt = 0.002  # picoseconds.
    
    for _ in range(n_steps):
        md.step(dt)
    
    snap = md.snapshots[len(md.snapshots) - 1]  # A/R.
    print(f"KE: {snap.energy_kinetic}, PE: {snap.energy_potential}, Atom posits:")
    for posit in snap.atom_posits:
        print(f"Posit: {posit}")
        # Also keeps track of velocities, and water molecule positions/velocity
    
    # Do something with snapshot data, like displaying atom positions in your UI.
    # You can save to DCD file, and adjust the ratio they're saved at using the `MdConfig.snapshot_setup`
    # field: See the example below.
    for snap in md.snapshots:
        pass
        
        
main()

Example use (Rust):

use std::path::Path;

use bio_files::{MmCif, Mol2, md_params::ForceFieldParams};
use dynamics::{
    ComputationDevice, FfMolType, MdConfig, MdState, MolDynamics,
    params::{FfParamSet, prepare_peptide},
    populate_hydrogens_dihedrals,
};

/// Set up dynamics between a small molecule we treat with full dynamics, and a rigid one
/// which acts on the system, but doesn't move.
fn setup_dynamics(
    mol: &Mol2,
    protein: &MmCif,
    param_set: &FfParamSet,
    lig_specific: &ForceFieldParams,
) -> MdState {
    let mols = vec![
        MolDynamics {
            ff_mol_type: FfMolType::SmallOrganic,
            atoms: &mol.atoms,
            // Pass a &[Vec3] of starting atom positions. If absent,
            // will use the positions stored in atoms.
            atom_posits: None,
            bonds: &mol.bonds,
            // Pass your own from cache if you want, or it will build.
            adjacency_list: None,
            static_: false,
            // This is usually mandatory for small organic molecules. Provided, for example,
            // in Amber FRCMOD files. Overrides general params.
            mol_specific_params: Some(lig_specific),
        },
        MolDynamics {
            ff_mol_type: FfMolType::Peptide,
            atoms: &protein.atoms,
            atom_posits: None,
            bonds: &[], // Not required if static.
            adjacency_list: None,
            static_: true,
            mol_specific_params: None,
        },
    ];

    MdState::new(&MdConfig::default(), &mols, param_set).unwrap()
}

fn main() {
    let dev = ComputationDevice::Cpu;
    let param_set = FfParamSet::new_amber().unwrap();
    
    let mol = Mol2::load(Path::new("../CPB.mol2")).unwrap();
    let mut protein = MmCif::load(Path::new("../1c8k.cif")).unwrap();
    let lig_specific = ForceFieldParams::load_frcmod(Path::new("../CPB.frcmod")).unwrap();
    
    // Or, if you have a small molecule available in Amber Geostd, load it remotely:
    // let data = bio_apis::amber_geostd::load_mol_files("CPB");
    // let mol = Mol2::new(&data.mol2);
    // let lig_specific = ForceFieldParams::from_frcmod(&data.frcmod);
    
    // Add Hydrogens, force field type, and partial charge to atoms in the protein; these usually aren't
    // included from RSCB PDB. You can also call `populate_hydrogens_dihedrals()`, and
    // `populdate_peptide_ff_and_q() separately.
    prepare_peptide(
        &mut protein.atoms,
        &mut protein.residues,
        &mut protein.chains,
        &param_set.peptide_ff_q_map.as_ref().unwrap(),
        7.0,
    )
        .unwrap();

    let mut md = setup_dynamics(&mol, &protein, &param_set, &lig_specific);

    let n_steps = 100;
    let dt = 0.002; // picoseconds.

    for _ in 0..n_steps {
        md.step(&dev, dt);
    }

    let snap = &md.snapshots[md.snapshots.len() - 1]; // A/R.
    println!(
        "KE: {}, PE: {}, Atom posits:",
        snap.energy_kinetic, snap.energy_potential
    );
    for posit in &snap.atom_posits {
        println!("Posit: {posit}");
        // Also keeps track of velocities, and water molecule positions/velocity
    }

    // Do something with snapshot data, like displaying atom positions in your UI.
    // You can save to DCD file, and adjust the ratio they're saved at using the `MdConfig.snapshot_setup`
    // field: See the example below.
    for snap in &md.snapshots {}
}

Example of loading your own parameter files:

    param_paths = ParamGeneralPaths(
        peptide=Some("parm19.dat"),
        peptide_mod=Some("frcmod.ff19SB"),
        peptide_ff_q=Some("amino19.lib"),
        peptide_ff_q_c=Some("aminoct12.lib"),
        peptide_ff_q_n=Some("aminont12.lib"),
        small_organic=Some("gaff2.dat")),
    )
    
    param_set = FfParamSet(param_paths)

    let param_paths = ParamGeneralPaths {
        peptide: Some(&Path::new("parm19.dat")),
        peptide_mod: Some(&Path::new("frcmod.ff19SB")),
        peptide_ff_q: Some(&Path::new("amino19.lib")),
        peptide_ff_q_c: Some(&Path::new("aminoct12.lib")),
        peptide_ff_q_n: Some(&Path::new("aminont12.lib")),
        small_organic: Some(&Path::new("gaff2.dat")),
        ..default()
    };
    
    let param_set = FfParamSet::new(&param_paths);

An overview of configuration parameters.

let cfg = MdConfig {
    // Defaults to Langevin middle.
    integrator: dynamics::Integrator::VelocityVerlet,
    // If enabled, zero the drift in center of mass of the system.
    zero_com_drift: true,
    // Kelvin. Defaults to 310 K.
    temp_target: 310.,
    // Bar (Pa/100). Defaults to 1 bar.
    pressure_target: 1.,
    // Allows constraining Hydrogens to be rigid with their bonded atom, using SHAKE and RATTLE
    // algorithms. This allows for higher time steps.
    hydrogen_constraint: dynamics::HydrogenConstraint::Fixed,
    // Deafults to in-memory, every step
    snapshot_handlers: vec![
        SnapshotHandler {
            save_type: SaveType::Memory,
            ratio: 1,
        },
        SnapshotHandler {
            save_type: SaveType::Dcd(PathBuf::from("output.dcd")),
            ratio: 10,
        },
    ],
    sim_box: SimBoxInit::Pad(10.),
    // Or sim_box: SimBoxInit::Fixed((Vec3::new(-10., -10., -10.), Vec3::new(10., 10., 10.)),
};

Python config syntax:

cfg = MdConfig() // Initializes with defaults.

cfg.integrator = dynamics.Integrator.VelocityVerlet
cfg.temp_target = 310.
# etc

Using with GPU

Rust setup with cudarc. Pass this to the step function.

let ctx = CudaContext::new(0).unwrap();
let stream = ctx.default_stream();
let module = ctx.load_module(Ptx::from_src(dynamics::PTX)).unwrap();
let dev = ComputationDevice::Gpu((stream, module));

Note: Currently GPU isn't supported in the python bindings

To use with an Nvidia GPU, enable the cuda feature in Cargo.toml. The library will generate PTX instructions as a publicly exposed string. Set up your application to use it from dynamics::PTX. It requires CUDA 13 support, which requires Nvidia driver version 580 or higher.

On unflattening trajactory data

If you passed multiple molecules, these will be flattened during runtime, and in snapshots. You will need to unflatten them if placing back into their original data structures.

Why this when OpenMM exists?

This library exists as part of a larger Rust biology infrastructure effort. It's not possible to use OpenMM there due to the language barrier. This library currently only has a limited subset of the functionality of OpenMM. It's unfortunate that, as a society, we've embraced a model of computing replete with obstacles. In this case, the major the obstacle is the one placed between programming languages.

While going around this obstacle, but would like to jump over others in the process to making molecular dynamics accessible. This includes operating systems, software distribution, and user experience. We hope that this is easier to install and use than OpenMM; it can be used on any Operating system, and any Python version >= 3.10, installable using pip or cargo.

This library is intended to just work. OpenMM itself is easy to install with Pip, but the additional libraries it requires to load force fields and files are higher-friction. Additionally, it's easy to run into errors when using it with proteins from RCSB PDB, and small molecules broadly. Getting a functional OpenMM configuration involves work which we hope to eschew here.

Compiling from source

It requires these Amber parameter files to be present under the project's resources folder at compile time. These are available in Amber tools. Download, unpack, then copy these files from dat/leap/parm and dat/leap/lib:

• amino19.lib
• aminoct12.lib
• aminont12.lib
• parm19.dat
• frcmod.ff19SB
• gaff2.dat
• ff-nucleic-OL24.lib
• ff-nucleic-OL24.frcmod
• RNA.lib

We provide a copy of these files for convenience; this is a much smaller download than the entire Amber package, and prevents needing to locate the specific files. Unpack, and place these under resources prior to compiling.

To build the Python library wheel, from the python subdirectory, run maturin build. You can load the library locally for testing, once built, by running pip install .

Eratta

• Python is CPU-only

• GPU operations are slower than they should, as we're passing all data between CPU and GPU each time step.

• CPU SIMD unsupported

References

• Amber forcefields
• Amber reference manual
• Ewald Summation/SPME
• OPC water model