Analyzing protein dynamics
Analyze a molecular dynamics simulation trajectory of the
closed-to-open transition of AdK [Beckstein2009].
Molecular dynamics glossary
- force field
- The force field is the collection of parameters that are needed to
describe the interactions between atoms in the system. Typically,
it contains bonded and non-bonded terms.
- frame
- One time step in a trajectory is also called a “frame” as in one
frame of a movie. A single frame contains one set of coordinates.
- topology (file)
- The topology file contains information about the atoms in the
simulation: a list of atom names and numbers, the kind of atom, the
bonds between atoms, and often additional information such as force
field related properties (e.g., partial charges, bond strengths,
Lennard-Jones parameters, ...). In the examples here we use the
widely used PSF format.
- trajectory (file)
A trajectory is a file that contains the positions of all atoms for
a number of time steps (or frames). The positions are ordered as
to correspond to the list of atoms in the topology
file. Trajectory files can come in many, many different formats;
each MD program produces trajectories in its own format. Examples
for trajectory formats are DCD and XTC.
In order to read a trajectory, a corresponding (and matching)
topology file is always needed.
Analyzing MD trajectories