Sir, thanks for your reply.... Yes I should have limited number of structure for a given point(pc1,pc2) but in my case, I have taken pc1 and pc2 as a range of points where the minima in FEL lies rather than a single point.So I think it would be relevant to apply the clustering as per your suggestion.Please let me know whether I am correct or not.. But which clustering method would be better for clustering my MD trajectories is also a question for me. I read some papers in which they have mentioned that the average linkage method works well for most of the cases, is it same to the gromacs linkage method of clustering?
Please provide your suggestion. On Sat, Sep 10, 2011 at 13:35, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > Hi Bipin, > > The averages from (2) and (3) are the same and may be far from realistic. > Minimizing an average structure may not always yield a structure that is > relevant or representative of the ensemble. I would suggest clustering > But you should only have a limited number of structures for a given point > (pc1,pc2), so why not just visualize the ensemble? > > Hope it helps, > > Tsjerk > > On Sep 10, 2011 8:02 AM, "bipin singh" <bipinel...@gmail.com> wrote: > > Hello, > > I have constructed a 2-d FEL using PC1 and PC2 as the reaction > coordinates(by using g_sham). > >From this 2-d FEL, I extracted the PC1 and PC2 (principal components) > values corresponding to minimum free energy. > Then I extracted the time during which system possess these PC's > values( by looking at PC Vs time plot). > Now I want to extract representative structures from these time > length(for eg. 40ns to 70 ns) of MD trajectories. > > > This question had been discussed previously but I am not able to find > a consensus solution: > > There are three approaches discussed in the previous posts: > (1)Use g_cluster with options -av(writes average) -cl and then > minimize the structure > (2)Use g_covar -av, and then minimize the average structure. > (3)Use g_rmsf -ox, and minimize the structure > > > Please suggest which approach should be used for this purpose. > > > > > -- > ----------------------- > Thanks and Regards, > Bipin Singh > -- > 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 > > -- > 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 > -- ----------------------- Thanks and Regards, Bipin Singh -- 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
