VMD-L Mailing List

From: hl332_at_drexel.edu
Date: Tue May 15 2007 - 10:32:17 CDT

Hi all,
  I have been trying to do the following task:

1. Calculating position of center_of_masss of my protein relative to whole system center_of_mass.
i wrote a small script like this: (in this script center_of_mass is another 'proc' sourced before)

set outfile [open coord.dat w];
set nf [molinfo top get numframes]
set sel1 [atomselect top "protein or type ZN"]
set sel2 [atomselect top "all"]
for {set i 0 } {$i < $nf } { incr i } {
    $sel1 frame $i
    $sel2 frame $i
    set protein [center_of_mass $sel1]
    set all [center_of_mass $sel2]
    set relative [vecsub $protein $all]
    puts $outfile "$relative"
 }
close $outfile
Now I have new coordinates of C.O.M of protein relative to whole system.

But i need this presently:

1. MOve the C.O.M of protein to this new position.

2. AND write a DCD file so that i can see absolute motion of protein when I already subtracted C.O.M of whole system from its (protein) C.O.M position

Any help to add these two-three modifying lines in my script will do great.

Thanks in advance

Harish

-------------------------------------------------
Harish Vashisth (Ph.D Candidate)
CAT-361,Chemical & Biological Engg.
Drexel University, Philadelphia, PA
office: 215-895-5823