Struct MdConfig 

pub struct MdConfig {

    pub integrator: Integrator,
    pub zero_com_drift: bool,
    pub temp_target: f32,
    pub pressure_target: f32,
    pub tau_pressure: f32,
    pub hydrogen_constraint: HydrogenConstraint,
    pub snapshot_handlers: SnapshotHandlers,
    pub sim_box: SimBoxInit,
    pub solvent: Solvent,
    pub max_init_relaxation_iters: Option<usize>,
    pub neighbor_skin: f32,
    pub overrides: MdOverrides,
    pub water_template_path: Option<String>,
    pub skip_water_pbc_filter: bool,
    pub spme_mesh_spacing: f32,
    pub spme_alpha: f32,
    pub coulomb_cutoff: f32,
    pub lj_cutoff: f32,
    pub energy_minimization_tolerance: f32,
}

This is the primary way of configurating an MD run. It’s passed at init, along with the molecule list and FF params.

Fields

integrator: Integrator

Defaults to Velocity Verlet.

zero_com_drift: bool

If enabled, zero the drift in center of mass of the system.

temp_target: f32

Kelvin. Defaults to 310 K.

pressure_target: f32

Bar (Pa/100). Defaults to 1 bar.

tau_pressure: f32

ps. Defaults to 5; this is what GROMACS uses.

hydrogen_constraint: HydrogenConstraint

Allows constraining Hydrogens to be rigid with their bonded atom, using SHAKE and RATTLE algorithms. This allows for higher time steps.

snapshot_handlers: SnapshotHandlers

sim_box: SimBoxInit

solvent: Solvent

max_init_relaxation_iters: Option<usize>

Prior to the first integrator step, we attempt to relax energy in the system. Use no more than this many iterations to do so. Higher can produce better results, but is slower. If None, don’t relax.

neighbor_skin: f32

Distance threshold, in Å, used to determine when we rebuild neighbor lists. 2-4Å are common values. Higher values rebuild less often, and have more computationally-intense rebuilds. Rebuild the list if an atom moved > skin/2.

overrides: MdOverrides

water_template_path: Option<String>

Optional path to a pre-equilibrated water template file. When set, this template is used instead of the built-in 60 Å template. A box-specific template (e.g. 30 Å) is required for accurate initial pressures, because the built-in template is cut from a larger equilibrated cell and lacks the long-range Coulomb correlations appropriate for the target PBC cell size. Generate one with the generate_water_init_template test (marked #[ignore]).

skip_water_pbc_filter: bool

Skip the PBC-boundary proximity check (2.8 Å cross-boundary O-O filter) when placing water molecules. Use this only when generating a pre-equilibrated template at the correct density: the ~88 boundary molecules that the filter would otherwise reject are needed to reach 1 g/cm³, and the MD equilibration run will push them to their natural distances.

spme_mesh_spacing: f32

SPME mesh spacing in Å. Smaller = higher-resolution reciprocal mesh, more accurate but slower. 1.0 Å is a good default; equivalent to GROMACS fourierspacing = 0.1 nm.

spme_alpha: f32

A bigger α means more damping, and a smaller real-space contribution. (Cheaper real), but larger reciprocal load. Common rule for α: erfc(α r_c) ≲ 10⁻⁴…10⁻⁵ Å^-1. 0.35 is good for cutoff of 10–12 Å.

coulomb_cutoff: f32

The distance at which we cut off short-range (Direct) Coulomb operations, and transtion to SPME reciprical forces. Å

lj_cutoff: f32

A hard distance cutoff for VDW forces. Å

energy_minimization_tolerance: f32

Simliar to GROMACS’ emtol. kcal mol⁻¹ Å⁻¹

Implementations

impl MdConfig

pub fn to_gromacs(&self, n_steps: usize, dt: f32) -> MdpParams

Creates a similar config for use with GROMACS. Attempts to replicate this library’s settings where we don’t have an applicable MdConfig field.

Not From trait: This lib depends on bio_files, but not the other way around.

pub fn save_mdp(&self, path: &Path, n_steps: usize, dt: f32) -> Result<()>

Convenience function to save in Gromacs’ .mdp format.

pub fn load_from_mdp(path: &Path) -> Result<Self>

Trait Implementations

impl Clone for MdConfig

fn clone(&self) -> MdConfig

Returns a duplicate of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for MdConfig

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl Default for MdConfig

fn default() -> Self

Returns the “default value” for a type.

impl From<MdpParams> for MdConfig

fn from(p: MdpParams) -> Self

Converts to this type from the input type.

impl PartialEq for MdConfig

fn eq(&self, other: &MdConfig) -> bool

Tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Rhs) -> bool

Tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl StructuralPartialEq for MdConfig