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
