Dear Gromacs users; I have generated Gibbs free energy landscapes from the two first principal components PC1 and PC2 obtained from Dihedral Principal Component analysis performed using Gromacs.
So, now I have a file *"shamlog-1_2.log" *that contain a list of the bins ordered by energy, for example : Minima sorted after energy Minimum 0 at index 40 energy 0.000 Minimum 1 at index 641 energy 0.146 (...) and I have another file *bindex-1_2.ndx* that shows the frames contained in each bin. Now I do not know how to proceed from here. How do I select the best bins? and then how do I select the best frames from those bins? Should I use all the frames of the selected bins and obtain like an average structure? Kindly, Lazaro -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
