############################
# This Tcl script counts the number of oil atoms within 3.6 angstrom of kerogen surface
# non-polar oil: OCT
# surface: KER
# created by Zelong Zhang in 2020
# https://er1czz.github.io/vmd/
############################
set output [open "count_out.txt" w]
set frames [molinfo top get numframes]
# loop
for {set i 0} {$i<$frames} {incr i} {
set a [atomselect top "resname OCT and within 3.6 of resname KER" frame $i]
set num [$a num]
puts "Frame: $i $num"
puts $output "$i $num"
$a delete
}
puts "Bingo!"
puts "Your data have been saved to the output file: count_out.txt"
puts "format as:"
puts "frame id, number of atoms"
close $output