sunita gupta wrote:
Hello
I have a query that how to do PCA which further includes *plotting the
displacement of each C-alpha along first eigenvector having largest
eigenvalue*. I read in many articles that this can be done using
gromacs. I did my MD simutaion using charmm forcefield and NAMD. I have
converted my *dcd file trr* and using *g_covar *covariance analysis. But
i am not getting anything regarding displacement calculation....
In GROMACS 3.1 manual their is an option of *-disp* is given with
*g_anaeig* command...but in 3.2 and 3.3. no such information is given
and its considering as invalid argument.
Also someone mailed me that calculating the displacement along
eigenvectors is same as rmsf (root mean square fluctuation) and it can
be calculated using -rmsf option in g_anaeig commant......Kindly help me
in this regard and clear my doubts...
g_anaeig -rmsf
seems a perfectly valid suggestion to me. What's your doubt?
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
http://www.mpibpc.mpg.de/groups/de_groot
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