.. -*- coding: utf-8 -*-
.. |->| replace:: →

============================
 Analyzing protein dynamics
============================

Analyze a molecular dynamics simulation trajectory of the
closed-to-open transition of AdK [Beckstein2009]_.

Download the **topology file** *adk.psf* and the **trajectory file**
*adk_dims.dcd* from
https://becksteinlab.physics.asu.edu/pages/courses/2016/PHY542/practicals/vmd/files/
.


Visualization
=============

- load *adk.psf* with *adk_dims.dcd* (use *load all at once*, this is faster
  in general)

- color domains and show as *new cartoon*

  - ``resid 30 to 59``: blue (NMP)
  - ``resid 122 to 159``: yellow (LID)
  - ``not (resid 30 to 59 122 to 159)`` (or ``resid 1 to 29 60 to 121
    160 to 214``): gray (CORE)

- play (loop: rock) (use the triangle button on the main VMD window)


RMSD change
===========

- RMSD change over the trajectory: Extensions |->| Analysis |->| RMSD Trajectory Tool
- Is the result consistent with the result of your :ref:`RMSD
  analysis of the static structures <Tertiary_structure>`?


Measuring distances
===================

Measure distances interactively: 
  
* '2' (or Mouse |->| Label |->| Bonds)

* click tip of LID and tip of NMP

* play the trajectory: label changes dynamically

* Graphics |->| Labels: Bonds

  - select
  - Graph (preview)
  - Graph...

* try different distances between residues (use the CA) and plot together:
  which change, which don't?
  
  - What would be good distances to report on conformational changes,
    e.g. for FRET_?  

  - Try also [Beckstein2009]_

    - I52-K145
    - A55-V169
    - A127-A194

.. _FRET: http://en.wikipedia.org/wiki/F%C3%B6rster_resonance_energy_transfer