VMD-L Mailing List

From: ramya narasimhan (ramya_jln_at_yahoo.co.in)
Date: Wed Dec 10 2008 - 01:31:38 CST

Hi All,
       I tried to find the center of mass for all the frames (2000) of the dcd file. The output contains only for 1966 frames. But when I move the frame in VMD and measure in Tkconsol, it is calculating for the rest. To check I save the coordinates in pdb format. I loaded the pdb and tried in the same way. It results in same manner. I have given the script below

set out [open com.dat w]
set numframes [molinfo top get numframes]
set sel2 [atomselect top protein]
 for {set frame 0} {${frame} < ${numframes}}  {incr frame} {
    $sel2 frame $frame
    set com [measure center ${sel2} weight mass]
    puts $out "center of mass of structure ${frame} is {$com}"
}

is there any mistake in the script?
Is it possible to find for many residues at the same time (like selecting resid 3 6 7 9 ... for each frame)?

Thanks in advance.
Ramya.L.