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

-- 

================================================================== 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 ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu