.. -*- coding: utf-8 -*-

============================
 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.



File downloads
==============

From
https://becksteinlab.physics.asu.edu/pages/courses/2016/PHY542/practicals/md/files/ download

1. the **topology file** *adk.psf* and the **trajectory file**
   *adk_dims.dcd*;

2. the **topology file** *1ake_nowater.psf* and the **trajectory file**
   *1ake_nowater.xtc*.


Analyzing MD trajectories
=========================

.. toctree::
   :maxdepth: 1

   visualization
   rmsd_fitting
   distances
   exercises