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The strength of the solvent-mediated attraction between a receptor and a
It is the thermodynamic "driving force" behind binding
The three-dimensional structure of a ligand or protein, specifically
referring to the spatial arrangements of atoms and molecular bonds in
Degrees of Freedom
In the context of simulations, degrees of freedom refer to all
independent coordinates and
that uniquely determine
the configuration of all atoms
in the simulation.
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
) 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.
for an in-depth discussion of floating point numbers.
A push or pull exerted on one object by another. Forces are important
as they drive changes in motion of objects.
Not to be confused with a set of forces
a force field in computational chemistry refers to set of
parameters used to calculate the
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.
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.
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
to describing how molecular dynamics simulations work.
Stored energy that can be transformed into motion or otherwise change
the properties of an object or system of objects.
The mathematical expression for potential energy, describing how
the conformation of a molecular system.
One copy (usually one of many) of a molecular system being simulated.
Substance that is dissolved in a solvent
that form a solution. In MD simulations, the ligand
and protein are considered the solutes.
Substance that dissolves a solute
different substance) to form a solution. The most common solvent is
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.
The set of conformations
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.
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)