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
