center of mass motion: problems

From: Vani Krishna (
Date: Thu Dec 08 2005 - 16:27:06 CST

Hi all,

I know this question has been asked before. But Iam
still a bit confused. I always observe a center of
mass motion drift if I do not wrap my system, atleast
initially. If a have such a trajectory and would like
to do analysis, I wanted to knwo the best way to go
about it.

(1) fitting all the frames wrt the initial frame and
then do the analysis

(2) move all the frames so that they are centered (tcl
below) and then do the analysis.

are there any suggestions out there? do people do
anything else to handle this problem?

 proc moveorigin {text} {
   set sel [atomselect top $text]
   set outfile stdout
   set out stdout
   set nf [molinfo [$sel molid] get numframes]
   puts "number of frames : $nf"

   set frame 0
   for {set i 0 } { $i < $nf } {incr i } {
      $sel frame $i
      $sel update
      set shift [measure center $sel]
      set c1 [lindex $shift 0]
      set c2 [lindex $shift 1]
      set c3 [lindex $shift 2]

      set c1 [expr -$c1]
      set c2 [expr -$c2]
      set c3 [expr -$c3]

      set shiftnew "$c1 $c2 $c3"
      $sel moveby $shiftnew



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