[gmx-users] normal mode analysis

Bert de Groot bgroot at gwdg.de
Wed Sep 18 09:25:29 CEST 2002

Nguyen Hoang Phuong wrote:
> Dear All,
> in the normal mode analysis of GROMACS, are the translation and rotation
> separated out before calculating the Hessian?

If I remember well the Hessian is calculated only using the internal 
coordinates, and then the overall translation and rotation should appear
with zero eigenvalues after diagonalisation. 


Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Theoretical molecular biophysics group
Am Fassberg 11 
37077 Goettingen, Germany

tel: +49-551-2011306, fax: +49-551-2011089

email: bgroot at gwdg.de

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