[gmx-users] normal mode analysis

[Bert de Groot]

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. 

Bert

____________________________________________________________________________
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
http://www.mpibpc.gwdg.de/abteilungen/071/bgroot
____________________________________________________________________________