MD Trajectories Visualization

While data of MD trajectory is the most important part of an analysis, animations of MD trajectory can be very intuitive and helpful to convey science than pure data alone. VMD is super handy in generating high-quality images and animations.

Basic steps

To produce an image/animation:

1. load the trajectory file (e.g., the .gro and .xtc file);
2. select different groups of atoms;
3. assign Drawing Method, Coloring Method, and Material for each selected group;
4. render image;
5. make animations from rendered images.

Here is an example code in the VMD console (Extensions -> tk Console):

  
# select polymer and use Licorice for Drawing Method, Name for Coloring Method, AOChalky for Material
resname PE1 PE2 PE3

# select water and use Licorice for Drawing Method, Name for Coloring Method, AOChalky for Material
resname SOL

# add hydrogen bonds and use HBonds for Drawing Method, ColorID (7 or green) for Coloring Method
resname PE1 PE2 PE3 or same residue as {resname SOL and within 3.5 of resname {PE1 PE2 PE3}}
  

Here is the rendered image:

Another rendered image of PEO-grafted gold nanopore:

where water is shown in Transparent blue, gold nanopore is represented by yellow QuickSurf and AOChalky for Material while polymer is drawn by Licorice Drawing Method, colored by Name and using AOChalky for Material.