[gmx-users] Trajectory analysis

[Bert de Groot]

Oleg Katchanov wrote:
> I want to get the information about the
> slow-freequency motion in the peptide molecule? How I understand, it
> must be the normal mode analysis - the art of harmonic analysis, or the
> covariance analysis of the trajectory matrix. 

for analysing your simulation, you want g_covar/g_anaeig. Normal
modes is a different type of calculation, NOT a trajectory analysis. 

> 
> g_covar -f traj.xtc -s topol.tpr -o eigenval.xvg -v eigenvec.trr -av
> average.pdb
> 

so far so good

> 
> ngmx -f eigenvec.trr -s topol.tpr
> 

you cannot visualise your eigenvectors directly with ngmx. ngmx is a trajectory viewer.
Usually, you'll want to run g_anaeig after g_covar. use -filter or -extr to
get the large-amplitude (often low-frequency) motions filtered from your MD
trajectory. The manual describes these options (and many more!) in more detail.


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
____________________________________________________________________________