From: Monika Madhavi (
Date: Fri Jul 03 2015 - 05:39:57 CDT

Dear all,

I have a big dcd file which does not fit into my memory. I want to select
few molecules from all the frames of my trajectory and save their
coordinates to a separate pdb file. I wrote a tcl script and it works fine
when I can load the whole trajectory at once (small dcd files) but, I don't
understand how can I use bigdcd with my script.

The guide on web says "The analysis script must accept one argument" which
I don't understand. My script takes two input arguments. Does this mean I
can't use bigdcd with this script?

proc trace {nt seltext } {
set n [molinfo top get numframes]
set selection {}
for {set i 0} {$i <$nt} {incr i} {
set ind [expr rand()*10000]
lappend selection $ind
set atomlist [atomselect top "index $selection"]

animate write pdb traced.pdb beg 0 end [expr $n-1] waitfor all sel $atomlist
$atomlist delete

I would be grateful if someone can suggest me how to use bigdcd with this


W.A.Monika Madhavi
Lecturer (Probation),
Department of Physics,
University of Colombo.