[gmx-users] Normal Mode Analysis on Calphas only ??

[Bert de Groot]

Hi,

Berk is right, you need to diagonalise the full Hessian.
Not only because of the minimisation but also because
of the coupled interactions via other atoms in the Hessian,
which would be neglected by diagonalising a CA-only
Hessian.

Deriving CA-eigenvectors from the Hessian eigenvectors
can be done approximately by extracting CA components from
the full vectors, but if you require a fully orthogonal set
then the easiest procedure for now (awating the formula Berk
mentioned) is to generate an ensemble based on the normal
modes with g_nmens and do a CA PCA on that.

Bert

________________________________________________
Bert de Groot, PhD

Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
37077 Goettingen, Germany

tel: +49-551-2012308, fax: +49-551-2012302

email: bgroot at gwdg.de
http://www.mpibpc.mpg.de/groups/de_groot