VMDscript.tcl

# Load the HIV-1 Protease
mol new 1_structure.psf waitfor all
mol addfile 1_system.1.4.dcd waitfor all

# Zoom by 2x
scale by 2.0

# Select protein, to be displayed
mol modselect 0 0 protein

# Represent as New Cartoon
mol modstyle 0 0 NewCartoon 0.300000 10.000000 4.100000 0

# Color by Secondary Structure
mol modcolor 0 0 Structure

# Render a figure "image.png"
## Enable shadowns and ambient occlusion
display shadows on
display ambientocclusion on

## Use Tachyon to render.
render TachyonInternal image.png

# Calculate RMSD over all frames and save to rmsd.csv
## Create a selection
set sel [atomselect top protein]

set ref [atomselect top protein frame 0]

set fileId [open "rmsd.csv" w]
puts $fileId "Frame,RMSD"
for {set i 0} {$i < [molinfo top get numframes]} {incr i} { 
  $sel frame $i
  puts $fileId "$i,[measure rmsd $sel $ref ]"
} 
close $fileId