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

================================
Visualization of MD trajectories
================================

Loading a MD trajectory
=======================

Load topology *adk.psf* with trajectory *adk_dims.dcd*.

.. Note:: You always load a topology file first and *then* you load
   the trajectory data for the system.

- **load the topology file:**
  :menuselection:`File --> New Molecule`    

  * :guilabel:`Load files for:` *New Molecule*
  * :guilabel:`Filename` *adk.psf*
  * :guilabel:`Determine file type`: *Automatically*

- **load the trajectory file:** In the :guilabel:`Molecule File
  Browser` 
  
  * :guilabel:`Load files for:` *0: adk.psf*
  * :guilabel:`Filename` *adk_dims.dcd*
  * :guilabel:`Determine file type`: *Automatically*
  * :guilabel:`Load all at once`: *x*

  (If you closed the :guilabel:`Molecule File Browser`, re-open it
  with :menuselection:`File --> New Molecule`.)  

.. Note:: Instead of using :menuselection:`File --> New Molecule` you
   can also select (highlight) your molecule in the main window (left
   click) and then use the :menuselection:`File --> Load Data Into
   Molecule` menu item.

Visualize
=========

- see `Visualizing protein structure and topology`_ from the previous
  practical for generally useful VMD settings and more details on
  selections and representations

- :menuselection:`Graphics --> Representations`: color domains and
  show as *new cartoon*

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

.. _Visualizing protein structure and topology:
   https://becksteinlab.physics.asu.edu/pages/courses/2016/PHY542/practicals/vmd/structure/index.html

Play a trajectory
=================

VMD can show a trajectory frame by frame. Trajectory play is
controlled through the main window.

- play with the :guilabel:`▶`  the right triangle button
- set :guilabel:`Loop` to :guilabel:`Rock` (makes trajectory move
  forward and backward)
- use the slider to manually move through the trajectory (note how the
  frame number changes)
- enter a new frame number in the frame number widget and press
  :kbd:`enter` to jump to the frame