7_even_md.vmd

#!/usr/local/bin/vmd
# VMD script written by save_state $Revision: 1.44 $
# VMD version: 1.9.1

##### Load traj
mol new 7_even_md.xyz waitfor all
#### Add representations
mol delrep 0 top

mol representation DynamicBonds 3.500000 0.300000 22.000000
mol color ColorID 8
mol selection {all}
mol material Goodsell
mol addrep top
mol selupdate 0 top 0
mol colupdate 0 top 0
mol scaleminmax top 0 0.000000 0.000000
mol smoothrep top 0 0
mol drawframes top 0 {now}

mol representation VDW 0.500000 27.000000
mol color ColorID 7
mol selection {name O}
mol material Glossy
mol addrep top
mol selupdate 1 top 0
mol colupdate 1 top 0
mol scaleminmax top 1 0.000000 0.000000
mol smoothrep top 1 0
mol drawframes top 1 {now}

mol representation VDW 1.500000 27.000000
mol color ColorID 0
mol selection {name H1}
mol material Glossy
mol addrep top
mol selupdate 2 top 0
mol colupdate 2 top 0
mol scaleminmax top 2 0.000000 0.000000
mol smoothrep top 2 0
mol drawframes top 2 {now}

mol representation VDW 1.500000 27.000000
mol color ColorID 1
mol selection {name H2}
mol material Glossy
mol addrep top
mol selupdate 3 top 0
mol colupdate 3 top 0
mol scaleminmax top 3 0.000000 0.000000
mol smoothrep top 3 0
mol drawframes top 3 {now}

mol representation DynamicBonds 6.000000 0.100000 22.000000
mol color ColorID 7
mol selection {all}
mol material Goodsell
mol addrep top
mol selupdate 4 top 0
mol colupdate 4 top 0
mol scaleminmax top 4 0.000000 0.000000
mol smoothrep top 4 0
mol drawframes top 4 {now}

#mol rename top 7_even_md.xyz
set viewpoints([molinfo top]) {{{1 0 0 -2.5966} {0 1 0 -9.81253} {0 0 1 -0.63547} {0 0 0 1}} {{1 0 0 0} {0 1 0 0} {0 0 1 0} {0 0 0 1}} {{0.067446 0 0 0} {0 0.067446 0 0} {0 0 0.067446 0} {0 0 0 1}} {{1 0 0 0} {0 1 0 0} {0 0 1 0} {0 0 0 1}}}
lappend viewplist [molinfo top]
set topmol [molinfo top]
#####

##### Load data from data file
set fp [open "population_7_even.dat" r]
set population [read $fp]
close $fp
set population_list [split $population "\n"]

set mol 0
set atoms [atomselect $mol all]
set n [ molinfo $mol get numframes ]

for {set i 0} {$i < $n} {incr i} {
    $atoms frame $i
    set pop_atom ""
    foreach c [$atoms get index] {
        set pop_frame [split [lindex $population_list $i]]
        lappend pop_atom [lindex $pop_frame $c]
    }
    $atoms set user $pop_atom
}
##### define user defined color method
mol modcolor 1 0 User
mol modcolor 2 0 User
mol modcolor 3 0 User