# Glossary

Find the FightAIDS@Home Phase 1 glossary here.

## New Terms

### Binding Affinity

The strength of the solvent-mediated attraction between a receptor and a ligand. It is the thermodynamic "driving force" behind binding reactions.

### Binding Free Energy

is a measure of binding affinity used in statistical mechanics.

### Conformation

The three-dimensional structure of a ligand or protein, specifically referring to the spatial arrangements of atoms and molecular bonds in 3D space.

### Degrees of Freedom

In the context of simulations, degrees of freedom refer to all independent coordinates and velocities that uniquely determine the configuration of all atoms in the simulation.

### Equilibrium

In the context of molecular dynamics simulations, equilibrium refers to the state in which no macroscopic change occurs in the system being simulated. In particular macroscopic thermodynamic quantities like temperature, pressure, and system energy remaining constant. Initially, the simulations most often start out of equilibrium and equilibrate slowly as the simulation continues. Developing methodologies to accelerate equilibration (sampling algorithms) is an active area of research.

### Floating Point Numbers

On computers, there needs to be a way to represent real numbers, including irrational (sqrt(2), Pi, etc.) and non-terminating rational (0.11111...) numbers, in binary. One representation is called floating point representation, where numbers are stored as two strings of digits, one representing the significant digits and the other representing the location of the decimal point. However, some numbers cannot be represented exactly as floating point numbers, and the difference between the exact number and its floating point representation is called floating point error. Floating point errors accumulate during computations in a way that can be considered random. See this webpage for an in-depth discussion of floating point numbers.

### Force

A push or pull exerted on one object by another. Forces are important as they drive changes in motion of objects.

### Force Field

Not to be confused with a set of forces, a force field in computational chemistry refers to set of potential functions and parameters used to calculate the potential energy of a system of atoms, bonds, and/or molecules in a simulation. You can think of a force field as all the information one would need to describe how all types of atoms and molecules interact with each other.

### Hamiltonian

The function used to compute the energy of a system. The Hamiltonian is usually a function of all position coordinates and velocities in a given system.

### Lambda

A tunable parameter in our Hamiltonian which controls how strongly the ligand and receptor interact with each other, ranging from totally uncoupled (lambda = 0) to fully coupled (lambda = 1).

### Molecular Dynamics Simulations

A class of computer simulation used to study the motion of a collection of atoms interacting via Newton's equations of motion. See the section on the main page dedicated to describing how molecular dynamics simulations work.

### Non-equilibrium

The opposite of equilibrium.

### Potential Energy

Stored energy that can be transformed into motion or otherwise change the properties of an object or system of objects.

### Potential Function

The mathematical expression for potential energy, describing how potential energy changes with the conformation of a molecular system.

### Replica

One copy (usually one of many) of a molecular system being simulated.

### Solute

Substance that is dissolved in a solvent that form a solution. In MD simulations, the ligand and protein are considered the solutes.

### Solvent

Substance that dissolves a solute (a different substance) to form a solution. The most common solvent is water.

### Statistical Mechanics

Physicists have solid theories which describe well the properties and motions of both the microscopic world (atomic collisions, molecule formation, etc.) and the macroscopic world (Newton's laws, concepts like pressure and temperature, etc.). However, in practical experience, one does not care (nor has a way to know) about all the microscopic details when checking the temperature in a room or sliding a box across the ground. Statistical mechanics provides the framework to bridge these two different perspectives by describing macroscopic quantities in terms of averages over microscopic behavior.

### Trajectory

The set of conformations a molecular system takes as a function of time throughout a simulation. During a simulation, the coordinates of all atoms are recorded at regular intervals, and when completed, the motions of the system can be represented in a movie format.

### Velocity

The rate of change of an object's displacement. Instantaneous velocity is speed at which an object moves in a given direction. Often an object's velocity is split into 3 components, it's velocity in the x (back and forth), y (left and right), and z (up and down) directions.