- Contemporary messages sorted: [ by date ] [ by thread ] [ by subject ] [ by author ] [ by messages with attachments ]

From: Lishan Yao <yaolisha.pilot.msu.edu>

Date: 13 Aug 2003 11:07:29 -0400

Thanks for your response. I think I understand why the determinant is 0

now. But then, first I do MD in constant energy. I don't need to remove

rotations. Second, why it always crashes in step 900? Does that mean

amber corrects rotation every 900 steps?

Best,

Lishan

On Wed, 2003-08-13 at 09:50, Andreas Svrcek-Seiler wrote:

*> 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: 13 Aug 2003 11:07:29 -0400

Thanks for your response. I think I understand why the determinant is 0

now. But then, first I do MD in constant energy. I don't need to remove

rotations. Second, why it always crashes in step 900? Does that mean

amber corrects rotation every 900 steps?

Best,

Lishan

On Wed, 2003-08-13 at 09:50, Andreas Svrcek-Seiler wrote:

-- Lishan Yao <yaolisha.pilot.msu.edu> MSU ----------------------------------------------------------------------- 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 - 16:53:01 PDT

Custom Search