[Xplor-nih] subtracting out translation

[Nikolai Skrynnikov]

We would like to subtract out protein's translational motion, but retain
rotational motion (assuming that with tcoupling=true the protein is not
going to spin out of control). We tried a few things, below is the version 
which seemed like our best bet:

  evaluate($count=1)

   while (2>1) loop write	
      evaluate ($TRAJECTORY = "traj_"+encode($count)+".dcd")
      dynamics torsion         
         ntrfrq = 0	
         timestep = 0.002  
         nstep = 5000         
         tcoupling = true    
         tbath = 300   
         nprint = 500
         iprfrq = 0
         asci = false
         nsavc = 500
         traj = $TRAJECTORY
      end
   evaluate ($count=$count+1)
   coor copy sele=(all) end
   coor orient sele=(all) end 
   display  $x $y $z
   
   coor swap sele=(all) end
   vector do (x=x+$x) (all)
   vector do (y=y+$y) (all)
   vector do (z=z+$z) (all)
{* alternaitvely coor translate sele=(all) vector=($x,$y,$z) end *}
   end loop write		


The printout from this script seems fine, but it actually fails to
reset the coordinates to (0,0,0) in between the frames as we hoped...

Many thanks ahead of time!

Cheers,

Nikolai

-- 
Nikolai R. Skrynnikov
Assistant Professor
Department of Chemistry
Purdue University
560 Oval Drive
West Lafayette, IN 47907-2084
USA

phone: 765 - 494 8519
fax: 765 - 494 0239
e-mail: nikolai at purdue.edu