Calculation of the evolution of the radius of gyration

xplor it is :

structure @native.psf end

evaluate ($first = 0)
evaluate ($step  = 1)

evaluate ($current = $first)

read trajectory

asci=false
input=fitted.dcd
begin=$first
skip=$step
stop=20000000
end

set display=gyration.list end

while ($status # "COMPLETE") loop traj

coor rgyration end
evaluate ($rg1 = $RG)

coor rgyration mass=true end

display $current $rg1 $RG

evaluate ($current =$current + $step)

read trajectory next end

end loop traj

stop

and then

xmgr -block gyration.list -bxy 1:2 -bxy 1:3

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You can also do the trick via a tcl script for vmd : see gyration.tcl.