AMBER Archive (2003)

Subject: Re: AMBER: constant energy simulation

From: David A. Case (case_at_scripps.edu)
Date: Wed Aug 13 2003 - 10:46:52 CDT

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 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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