[gmx-users] Eigenvalue values from PCA (a general question)

Hi all I have a query about the eigenvalue values obtained from g_covar and g_anaeig I performed essential dynamics using PCA on my system (Protein-DNA complex) considering BB of the protein and the phosphate and sugar of the DNA for a 50 ns trajectory. The eigenvalue which i do obtain for the

Re: [gmx-users] Eigenvalue values from PCA (a general question)

Hi Vijayan R., What i infer from this is that the cumulative variance experienced by  the top 10 PC is  hardly ~ 30 %. Not experienced...; It's the variance captured by the first ten PC's. a) does this imply inadequate sampling by MD or a limited conformational change happening  in the

Re: [gmx-users] Eigenvalue values from PCA (a general question)

Hi Tsjerk Many thanks for your response. Do you think NMA is worth considering in such cases like this? Regards Vijayan.R On Thu, Dec 15, 2011 at 3:39 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Vijayan R., What i infer from this is that the cumulative variance experienced by the

Re: [gmx-users] Eigenvalue values from PCA (a general question)

Hi Vijayan.R, Not really. NMA also assumes linear relationships. Cheers, Tsjerk On Thu, Dec 15, 2011 at 10:48 PM, R.S.K.Vijayan biovija...@gmail.com wrote: Hi Tsjerk Many thanks for your response. Do you think NMA is worth considering in such cases like this? Regards Vijayan.R On

Re: [gmx-users] Eigenvalue values from PCA (a general question)

Thanks Tsjerk On Thu, Dec 15, 2011 at 4:55 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Vijayan.R, Not really. NMA also assumes linear relationships. Cheers, Tsjerk On Thu, Dec 15, 2011 at 10:48 PM, R.S.K.Vijayan biovija...@gmail.com wrote: Hi Tsjerk Many thanks for your