Re: [gmx-users] Eigenvector and eigenvalues

Hi Ankitha, Taking the backbone for analysis doesn't give you more information than using only C-alphas. These are extremely correlated. Cheers, Tsjerk On Sun, Jun 9, 2013 at 5:28 PM, Ankita naithani ankitanaith...@gmail.comwrote: Hi Tsjerk, Thank you so much for the helpful insight. It

Re: [gmx-users] Eigenvector and eigenvalues

Hi Tsjerk, Thank you so much for the helpful insight. It will surely help in clearing some basic concepts about eigenvectors and the projections. Also, since in the end you mentioned about my matrix being derived only from C-alpha atoms which proves a limitation, would you reckon a backbone

Fwd: [gmx-users] Eigenvector and eigenvalues

Hi Tsjerk, [I am reposting it since my previous attachment was unable to proceed I guess] Thank you for the reply. I am sorry but I don't have the snapshots with me as my system was formatted and I lost that information. However, I performed PCA again on Calpha atoms and this time my matrix is

Re: [gmx-users] Eigenvector and eigenvalues

Hi Ankita, It is important to use the correct names for things. The projection is the (scalar) inner product of the configuration (coordinates) with the eigenvector. This is also named the score of the configuration on the selected eigenvector. With g_anaeig -proj you get the projection. Each

[gmx-users] Eigenvector and eigenvalues

Hi, I wanted to know about the eigenvectors and eigenvalues. I recently performed the principal component analysis (only the backbone into consideration) on a trajectory of 2000 residues. I obtained 15641 eigenvectors and 17928 eigenvalues. There is a difference in the number, which I am not

Re: [gmx-users] Eigenvector and eigenvalues

Hi Ankita, Please provide the commands you've run and the screen output from g_covar. Cheers, Tsjerk On Thu, Jun 6, 2013 at 3:44 PM, Ankita naithani ankitanaith...@gmail.comwrote: Hi, I wanted to know about the eigenvectors and eigenvalues. I recently performed the principal component