VMD-L Mailing List
From: Sangkha Borah (sborah53_at_gmail.com)
Date: Tue Mar 01 2016 - 10:18:58 CST
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Dear all,
I am trying to calculate the interatomic distances between various atom
pairs in a small periodic system containing an oxoanion dissolved in 60
water molecules (the same is also true for a crystalline solid). The
trajectory is wrapped about the origin. I wanted to use vmd/tcl script
using pbctools
The main part of the script goes like --
package require pbctools
pbc set {12.42 12.42 12.42} -all
set outfile [open "test.dat" w]
set nf [molinfo top get numframes]
set ind1 [atomselect top "index 1"]
set ind4 [atomselect top "index 4"]
for {set i 0} {$i < $nf} {incr i} {
$ind1 frame $i
$ind4 frame $i
set dis1_4 [veclength [vecsub [lindex [$ind4 get {x y z}] 0]
[lindex [$ind1 get {x y z}] 0] ]]
puts $outfile "$i \t $dis1_4 "
}
close $outfile
This script works!
But does it incorporate pbc while calculating the distance ?
My intuition is that it perhaps does not! At least the GUI version does not
do it.
Am I correct ?
If so, is there any other way to do so , like the one "pbwithin" instead
of within that is used to find the neighbours within a certain cutoff
distance using pbc.
Please help to clear my doubts.
Regards,
Sangkha Borah
IIT Guwahati, Assam, India
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