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From: Andreas Svrcek-Seiler <svrci.tbi.univie.ac.at>

Date: Wed, 13 Aug 2003 15:50:32 +0200 (CEST)

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

Date: Wed, 13 Aug 2003 15:50:32 +0200 (CEST)

Hi,

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

-- ))))) ((((( ( O O ) -------oOOO--(_)--OOOo----------------------------------------------------- o Wolfgang Andreas Svrcek-Seiler o (godzilla) svrci.tbi.univie.ac.at .oooO Tel.:01-4277-52733 ( ) Oooo. -------\ (----( )-------------------------------------------------------- \_) ) / (_/ ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber.scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo.scripps.eduReceived on Wed Aug 13 2003 - 15:53:00 PDT

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