> trajin traj.mdcrd 1 1000000 20
> center :1-125 mass origin
> image origin center familiar
> trajout traj_reimage.mdcrd
> go
>
> I also tried to use "rms first :1-125" and/or "unwrap :1-125" within the
> above script. (right before the "center" line)
You cannot do the rms command prior to imaging since this will rotate the
box and break the imaging process (since the box frame of reference is not
rotated).
Molecules do rotate naturally. If you want to see a movie or trajectory
without this rotation, you center/image first, and then do the RMS fit
with the RMS command. The box will rotate with the molecule.
--tec3
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Received on Wed Aug 24 2011 - 15:30:03 PDT
