#!usr/bin/tclsh
# analysis of the distance between the C- and N-termini of deca-alanine.
# to use this script, type in the command
# vmd -dispdev text -e analysis.vmd -args current_replica current_step
# current_step denotes the # of times the simulation has been restarted.

# read in command line arguments: first replica, then step
if {$argc != 3} {
  puts "Not enough arguments!"
  exit
}
set rep [lindex $argv 0]
set step [lindex $argv 1]

# load psf and trajectory
mol new ../alanin.psf type psf
mol addfile ../output/$rep/stretch_alanin.job$step.$rep.sort.dcd type dcd waitfor all

# define the distance. Notice that the atom ID in VMD starts from 0.
set a1 0; set a2 65

# Delete all existing bond labels so that the one we add has index 0. 
label delete Bonds
# Use the top molecule 
set molid [molinfo top] 
# Add the dihedral monitor 
label add Bonds $molid/$a1 $molid/$a2 
# Get all values 
set output [label graph Bonds 0] 

# write out the distance time series
set outFileName time_series/alanine_${step}_$rep.anal
set fileID [open $outFileName w]
foreach distance $output {puts $fileID $distance}
close $fileID

quit