[gmx-users] Re: plotting the displacement of each C-alpha along first eigenvector having largest eigenvalue

[Bert de Groot]

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