Thanks Micheal for pointing out the mistake On Fri, Dec 16, 2011 at 4:20 AM, Niesen, Michiel <mnie...@coh.org> wrote:
> >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 >
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