HyMD-tutorial

ideal_gas

Monoatomic particles with no interactions.

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Bonded interactions

ideal_chain

Monoatomic chains of particles connected by two-particle bonds.

rods

Monoatomic chains of particles connected by two-particle bonds with bending stiffness due to anglar three-particle bonds.

helixes

Monoatomic chains of particles connected by two-particle bonds and four-particle torsional bonds.

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Field interactions

phase_separation

Binary A/B monoatomic particles with χ-interactions.

copolymer

Diblock A/B co-polymer with two-particle bonds and three-particle bonds and χ-interactions.

lipid_self_assembly

Model DPPC with two-particle bonds and three-particle bonds and χ-interactions self-assembling into a bilayer.

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Electrostatic interactions

peptide

Model peptide with two-particle bonds and three-particle bonds and four-particle torsional bonds and χ-interactions and dipole reconstructed electrostatic interactions.

sds

Model SDS surfactant with two-particle bonds and three-particle bonds and χ-interactions and electrostatic interactions self-assembling into a micelle.