VMD

Visual Molecular Dynamics is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code.
It is useful to visualise trajectories.

The home page is: https://www.ks.uiuc.edu/Research/vmd/.

It is available on Aurora:
module load vmd/1.9.2

Simple use with Amber simulations

Left button rotates
Scrolling zooms in or out
c - allows you to centre on an atom with the mouse
t - allows you to translate your molecule
r - goes back to default rotation

Start VMD:
vmd
File - New molecule
Enter the prmtop file as the file name
and AMBER7 Parm as the file type
Load next a trajectory with the file type AMBER coordinates
In VMD Main, click on
Graphics - Representations - Create Rep
Here you can select a molecule
resname L01
or a surrounding
all and within 6 of resname L01

Visualization of the trajectory in VMD using the prmtop file as coordinate input results in water molecules with a bond between the two hydrogens when rigid water models such as TIP3P are used. To eliminate this bond, you can convert the coordinates to pdb format.