Abstract Representation of a Site in a Molecular Simulation Object

Site is the object that represents any general interaction site in a molecular simulation. Sites have been designed to be as general as possible, making no assumptions about representing atoms or beads, or having mass or charge. That is, a Site can represent an atom in an atomistic system, a bead in a coarse-grained system, and much more.

In general, a site in a molecular simulation can be of following types (braces represent potential form):

1. Atom (AtomType)
2. Bead (AtomType)
3. Virtual Site (None)
4. Point (None)

In this post We will try to explain what each of these sites mean in terms of modeling them. From that we will try to derive the properties and methods for common abstract representation of a site.

Atom and Its Potential Form

An atom is the fundamental form of a site with an element, mass and charge and other properties.
Properties of an Atom:

1. Name : Name for the atom (mandatory)
2. Position : Position (Cartesian Coordinates, unyt based) (mandatory, defaults)
3. Charge : Charge of the Atom (Optional)
4. Mass : Atomic Mass (Optional)
5. Element : Element (Optional)
6. AtomType : AtomType for the Site (The Potential Form)

Property preceedence when used with AtomType:

• Charge (Atom) > Charge (AtomType)
• Mass (Atom) > Mass (AtomType)

Bead and Its Potential Form

A bead is like an Atom without an Element, commonly used in coarse-grained simulations.
Properties of a Bead:

1. Name : Name for the bead (mandatory)
2. Position : Position (Cartesian Coordinates, unyt based) (mandatory, defaults)
3. Charge : Charge of the bead (Optional)
4. Mass : Bead Mass (Optional)
5. AtomType : AtomType for the Site (The Potential Form)

Property preceedence when used with AtomType:

• Charge (Atom) > Charge (AtomType)
• Mass (Atom) > Mass (AtomType)

Low Priority: Classmethod method to form a bead from group of Atoms.

Virtual Site or Dummy Atom and Its Potential Form

A virtual Site is a Site for which position is determined based on the position of individual atoms constituting the Virtual Site.
Properties for VirtualSite:

1. Name : Name for the virtual site (mandatory)
2. Charge : Charge of the virtual (Optional) (default = 0.0)
3. Mass : Atomic Mass (Optional) (default = 0.0)
4. AtomType : AtomType for the Virtual Site (The Potential Form) (default parameter values are zeros)

How to calculate position for a virtual site?

We either have a site groups in the class itself or a VirtualSitePosition class that handles calculating positions from Sites that form this virtual site.

Point Site and Its Potential Form

TBD..

Connection Rules between Various Types of Sites

• Atom - Atom = Bond
• Atom - Atom - Atom = Angle
• Atom - Atom - Atom - Atom = Dihedral or an Improper
• Bead - Bead = Bond
• Bead - Bead - Bead = Angle
• Bead - Bead - Bead - Bead = Dihedral or an Improper
• Bead - Atom = Bond
• Bead - Atom - Bead = Angle (any permutation)
• Bead - Atom - Bead - Atom = Dihedral or an Improper (any permutation)
• VirtualSite = Not allowed in any connections

Abstract Representation of a Connection in a Molecular Simulation Object

A Connection that stores data about connections between sites.

This class functions as a super-class for any connected groups (bonds, angles, dihedrals, etc).

Each instance can have a property for the conection_type (bond_type, angle_type, dihedral_type) which are the subclasses of an Abstract Potential Object

In general, a connection in a molecular simulation can be of following types (braces represent potential form):

1. Bond (BondType)
2. Angle (AngleType)
3. Dihedral (DihedralType)
4. Improper (ImproperType)
5. NSiteConnection (NSiteConnectionType) : 2 Body Potential, 3 Body Potential

Question: Is an abstraction that is higher than Connection needed to correctly encapsulate all associations and AssociationTypes?

Bond and Its Potential Form

A Bond is a 2 Site connection. See Connection Rules above for the possible Site connections that qualify as a Bond.
Properties of a Bond:

• Name : Name of the Bond
• Members : Set/tuple/list of length 2,
• Equivalent Members : A datastructure representing equivalent members (To be used by container/topology)
• BondType : A Potential object of type BondType

Angle and Its Potential Form

An Angle is a 3 Site connection. See Connection Rules above for the possible Site connections that qualify as an Angle.
Properties of a Angle:

• Name : Name of the Angle
• Members : Set/tuple/list of length 3,
• Equivalent Members : A datastructure representing equivalent members (To be used by container/topology)
• AngleType : A Potential object of type AngleType

Dihedral/Improper and their Potential Form

Both Dihedrals and Impropers represent a 4 Site connection. See Connection Rules above for the possible Site connections that qualify as an Improper/Dihedral.
Properties of a Dihedral/Improper:

• Name : Name of the Dihedral/Improper
• Members : Set/tuple/list of length 4,
• Equivalent Members : A datastructure representing equivalent members (To be used by container/topology)
• DihedralType/ImproperType : A Potential object of type DihedralType/ImproperType

How should we allow addition of Bonded Connections between the Sites? Should you be allowed to add an Angle between three sites A-B-C if there's no Bond A-B or B-C or equivalent?