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From: Monika Madhavi (monikamadhavi_at_gmail.com)
Date: Fri Jul 03 2015 - 05:39:57 CDT
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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
script.
Regards,
Monika
-- W.A.Monika Madhavi Lecturer (Probation), Department of Physics, University of Colombo.
- Next message: Mohsen Farshad: "pdb and topology files for DNA"
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- Next in thread: Morgan, Brittany: "RE: Using bigdcd for an already written script"
- Reply: Morgan, Brittany: "RE: Using bigdcd for an already written script"
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