# 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.

### 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.

### 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.