AMBER Archive (2009)

Subject: Re: [AMBER] Re: nab normal mode analysis has imaginary frequencies

From: case (
Date: Thu Dec 10 2009 - 08:46:20 CST

On Wed, Dec 09, 2009, Junmei Wang wrote:

> This is an update with the "image frequency" issue I posted a long time
> ago. When the 'ntrun' parameter in nmode() was set to 1 (using dsyevd
> routine to diagonalize the Hessian), all my 8 proteins had image
> frequencies. However, in recent when I set 'ntrun' to 0, which uses the
> dsyev routine to diagonalize the Hessian, all those image frequencies
> disappeared.

Wow! Thanks for the update...I'll look into it. I think most of my real
tests have used ntrun=0 or 2 for proteins. The problems with ntrun=1 don't
seem to show up for small molecules, but this certainly deserves a test.


AMBER mailing list