Struct MdConfig 

pub struct MdConfig {

    pub integrator: Integrator,
    pub zero_com_drift: bool,
    pub com_motion_removal: ComMotionRemoval,
    pub com_removal_interval: usize,
    pub temp_target: f32,
    pub barostat_cfg: Option<BarostatCfg>,
    pub hydrogen_constraint: HydrogenConstraint,
    pub snapshot_handlers: SnapshotHandlers,
    pub sim_box: SimBoxInit,
    pub solvent: Solvent,
    pub max_init_relaxation_iters: Option<usize>,
    pub energy_minimization_tolerance: f32,
    pub neighbor_skin: f32,
    pub solvent_template_type: SolventTemplateType,
    pub skip_water_pbc_filter: bool,
    pub spme_mesh_spacing: f32,
    pub spme_alpha: f32,
    pub coulomb_cutoff: f32,
    pub lj_cutoff: f32,
    pub recenter_sim_box: bool,
    pub overrides: MdOverrides,
}

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

Legacy on/off switch for COM motion removal. Use together with com_motion_removal and com_removal_interval.

com_motion_removal: ComMotionRemoval

GROMACS-style COM-motion removal mode.

com_removal_interval: usize

Interval, in steps, for COM-motion removal. GROMACS defaults to 100.

temp_target: f32

Kelvin. Defaults to 310 K.

barostat_cfg: Option<BarostatCfg>

None to disable it.

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

Sets the bounds for the entire simulation. This is used both to populate the solvent, and to set periodic boundary conditions for SPME computatations and general wrapping/min-image.

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.

energy_minimization_tolerance: f32

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

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.

solvent_template_type: SolventTemplateType

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

recenter_sim_box: bool

If enabled, keep the cell centered on the dynamic atoms at init and during the run. Disable this for pulling / driven systems where you want the box to remain fixed.

overrides: MdOverrides

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

Equality operator ==.

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

Inequality operator !=.

impl StructuralPartialEq for MdConfig