> It's likely I have much molecule that simulated, then I just want to lock one 
> of x-axis of an atom.

Use the "Select" tool to select an atom or atoms. Go to Extensions -> Molecular 
Mechanics -> Fix Selected atoms.

If you just want to lock the x-axis, then choose "Constraints…" instead of "Fix 
Selected" and freeze the x-coordinate. (It's possible.)

Hope that helps,
-Geoff

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