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

[Florian Haberl]

Hi,


On Thursday, 31. July 2008, sunita gupta wrote:
> hi, all
>
> 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 relevant

take a look at g_covar and g_anaeig  in the manual.

With g_covar you can calculate the (mass weighted) eigenvectors/ eigenvalues 
of your simulation, and this can be analysed further with g_anaeig, i think 
you mean the the RMSF fluctuations per atom of the eigenvectors which can be 
calculated with g_anaeig -rmsf

>
> Thanking in Anticipation


greetings,

Florian

-- 
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 Florian Haberl                        
 Computer-Chemie-Centrum   
 Universitaet Erlangen/ Nuernberg
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 Telephone:  	+49(0) − 9131 − 85 26573
 Mailto: florian.haberl AT chemie.uni-erlangen.de
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