Re: AMBER: constant energy simulation

From: Lishan Yao <>
Date: 13 Aug 2003 12:09:14 -0400

   I don't want to remove translation and rotation. But I don't know how
to do that.


On Wed, 2003-08-13 at 11:46, David A. Case wrote:
> On Tue, Aug 12, 2003, Lishan Yao wrote:
> > 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
> This is a bug: the code is not set up to handle a two-atom system. I'm not
> sure you need to remove translationa and rotation anyway. After running
> the simulation, you would use ptraj to do an rms superposition -- I _think_
> this would force the molecule to always "point" the same direction. Then
> you could run quasih to get the frequency.
> ..good luck....dac
Lishan Yao <>
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Received on Wed Aug 13 2003 - 17:53:01 PDT
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