AMBER Archive (2003)

Subject: Re: AMBER: constant energy simulation

From: Andreas Svrcek-Seiler (svrci_at_tbi.univie.ac.at)
Date: Wed Aug 13 2003 - 08:50:32 CDT

Hi,
> 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
origin.

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 = I.omega, 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

Andreas 

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                       svrci_at_tbi.univie.ac.at
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