>Date: Thu, 15 Dec 2011 15:11:12 -0500 >From: "R.S.K.Vijayan" <biovija...@gmail.com> >Subject: [gmx-users] Eigenvalue values from PCA (a general question) >To: gmx-users@gromacs.org >Message-ID: > <camm9pawrymqrgzheriarvovk7qwuzpfwrm_owc_0+cemezm...@mail.gmail.com> >Content-Type: text/plain; charset="iso-8859-1" > >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 top 10 >principal components are stated below > > 1 10.1064 > 2 4.78616 > 3 4.07406 > 4 3.48535 > 5 2.7176 > 6 2.13348 > 7 1.75909 > 8 1.45699 > 9 1.12932 > 10 0.893933 > >What i infer from this is that the cumulative variance experienced by the >top 10 PC is hardly ~ 30 %.
The cumulative variance described by a set of PCs is not the sum of their eigenvalues. You have to take the sum of the first x eigenvalues as a percentage of the sum of all eigenvalues to get the cumulative variance. >a) does this imply inadequate sampling by MD or a limited conformational >change happening in the system???? >b) is it wise to consider the Nucleic acid during essential dynamics or >should it be discared and only the Protein BB or CA be considered. > >Thanking you in advance for your suggestions. My apologies since it sound >to be a very general question and rather not very specific to Gromacs. > >Regards >Vijayan.R --------------------------------------------------------------------- *SECURITY/CONFIDENTIALITY WARNING: This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wish to receive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. --------------------------------------------------------------------- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
