Subject: Normal mode generation with CHARMm

From: Greg Lakatos <[email-masked]>
Date: Sun, 27 Aug 2000 06:52:51 -0700 (PDT)

Hello,

Recently I've started using CHARMm to calculate the normal modes of a
moderately sized macromolecule (1254 atoms), and have run into some
difficulty.

1) CHARMm only generates 3 modes with a 0 frequency whereas I was
expecting 6 modes with 0 frequency (3 rigid body translations, 3 rigid
body rotations)

2) CHARMm generates negative frequencies corresponding to negative
eigenvalues.  If CHARMm is diagonalizing the matrix
corresponding to the linearized equations of
motion, then shouldn't a negative eigenvalue give a complex frequency
(Non-oscillatory behavior)?  In any event, why generate negative
frequencies?

The normal modes were calculated with the molecule in its minimum energy
configuration through the use of the DIAG command.

Any help would be greatly appreciated.

Thanks,

Greg Lakatos
([email-masked])

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From: Christoph van Wüllen <[email-masked]>
Date: Sun, 27 Aug 2000 20:52:20 +0200

>expecting 6 modes with 0 frequency (3 rigid body translations, 3 rigid

you cannot expect zero frequency for the "linearized" rotational modes unless you are
*exactly* at a stationary point.
The "true" rotations of course can only be expressed in curvilinear coordinates, the
linearized ones will also stretch the bonds.

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