Hi Thomas, Whether or not it makes sense to do PCA on the domain only depends on the question you ask. It may well make sense if you aim at characterizing the intra-domain motions. But be aware that you will view those motions within the context of the rest of the protein. It is quite likely that the internal motions depend on the interaction with the surroundings.
Concerning the cosine content, there indeed seems to ba a transition. But that is already evident from your RMSD plot. A lot of stuff is still happening in the second half of the simulation. To see if the last part of your simulation is in a (local) equilibrium, you can calculate the average structure from that part, say the alst 10 or 20 ns, and determine the RMSD against the average. The RMSD should then decrease towards the average and level off or oscillate around it to assure you've reached some sort of equilibrium. On the basis of that you could then decide whether it's worthwhile performing PCA on that part only. Cheers, Tsjerk On Sat, Mar 10, 2012 at 3:18 PM, Thomas Evangelidis <teva...@gmail.com> wrote: > Regarding my second question, I have been experimenting with the cosine > content using different portions of the trajectory and these are the results > I got for the first principal component: > > proj-ev1_coscont_0-5ns.xvg 0.0174761 > proj-ev1_coscont_0-10ns.xvg 0.0283423 > proj-ev1_coscont_0-15ns.xvg 4.16906e-06 > proj-ev1_coscont_0-20ns.xvg 0.0689592 > proj-ev1_coscont_0-25ns.xvg 0.161691 > proj-ev1_coscont_0-30ns.xvg 0.298431 > proj-ev1_coscont_0-35ns.xvg 0.535732 > proj-ev1_coscont_0-40ns.xvg 0.767029 > proj-ev1_coscont_0-45ns.xvg 0.885829 > proj-ev1_coscont_0-50ns.xvg 0.906473 > > > proj-ev1_coscont_5-50ns.xvg 0.8823 > proj-ev1_coscont_10-50ns.xvg 0.751018 > proj-ev1_coscont_15-50ns.xvg 0.537473 > proj-ev1_coscont_20-50ns.xvg 0.357136 > proj-ev1_coscont_25-50ns.xvg 0.145889 > proj-ev1_coscont_30-50ns.xvg 0.0150995 > proj-ev1_coscont_35-50ns.xvg 0.00123905 > proj-ev1_coscont_40-50ns.xvg 0.00675679 > proj-ev1_coscont_45-50ns.xvg 0.0105643 > > > The total time I have run the simulation was 70ns, but judging from the > steep increase of the RMSD (RMSD plot attached), I decided to exclude the > first 20ns from the analysis. Hence the cosine content values above > correspond to the last 50ns and the counting starts from the 20th ns. > > Clearly the convergence of the last 50ns is not good > (proj-ev1_coscont_0-50ns.xvg: 0.906473), but the PC1 plot (attached) shows a > steep decrease at ~30ns which looks like a conformational transition. It is > also evident that the cosine content decreases drastically approximately at > that point (25-50ns: 0.145889, 30-50ns.xvg: 0.0150995, 35-50ns.xvg: > 0.00123905, etc.) and reached values that are not bad. > > Unfortunately, extending the simulation is not an option due to lack of time > (I am forced to finish the manuscript soon). So would you recommend doing > essential dynamics for the last 20ns? > > I would GREATLY appreciate any comments!!! > > Thomas > > > > On 7 March 2012 21:56, Thomas Evangelidis <teva...@gmail.com> wrote: >> >> >> Dear GROMACS community, >> >> I have two questions regarding PCA. I have run MD simulations for 70 ns >> for a protein of 1100 amino acids, of which I decided - based on the RMSD - >> to analyze the last 50. >> >> 1) The protein consists of 5 domains, out of which only one is of interest >> in this study. Is it right to do draw conclusion from PCA restricted that >> domain (400 aa)? >> >> 2) How can I find out if the simulation time is sufficient to do PCA? >> >> Thanks in advance for any feedback. >> >> Thomas >> >> > > > -- > 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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