[gmx-users] Re: plotting the displacement of each C-alpha along first eigenvector having largest eigenvalue
Bert de Groot
bgroot at gwdg.de
Fri Aug 1 10:05:20 CEST 2008
sunita gupta wrote:
> 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...
seems a perfectly valid suggestion to me. What's your doubt?
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
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