Re: AMBER: constant energy simulation

From: Andreas Svrcek-Seiler <>
Date: Wed, 13 Aug 2003 15:50:32 +0200 (CEST)

> I use amber7 to do MD constant energy simulation for a diatomic
> molecule. But I get something wrong here:
> ------------------------------------------------------------------------------
> %CENMAS-F-INERTIA_TENSOR, determinant is zero ... stop
> Can some one tell me what this tensor is and why the program is stopped?
Well, If I remember correctly, it's like the following:
1) Assume, for simplicity, that the center of mass coincides with the

2) Then, let L be the angular momentum of your system, which can be
calculated from the individual velocities (linear momenta) and positions.
Classical Mechanics teaches L =, where I is the tensor of inertia
and omega points in the direction of the 'momentary total rotation'.
Alas, I don't know the correct english name for omega.

3) To remove overall rotation, you have to invert I to get
omega = I^(-1).L . If your system is diatomic (or perfectly linear), I is
singular and that inversion fails.

4) If you swith off the heat bath early, there's no need to remove the
rotation, lengthy 'equilibration' of a diatomic molecule in vaccum
does not seem to be too useful.

Hope it helps,
good luck


           ( O O )
              o        Wolfgang Andreas Svrcek-Seiler  
              o        (godzilla) 
      .oooO            Tel.:01-4277-52733 
      (   )   Oooo.    
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Received on Wed Aug 13 2003 - 15:53:00 PDT
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