[gmx-users] Trajectory analysis

Bert de Groot bgroot at gwdg.de
Wed Feb 20 12:50:57 CET 2002

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.


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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