Hi all , When performing a PCA of two different ensembles of the same molecule the atoms of each molecule need to be in the same order ( same atom name associated to the same index) right ?
However, my two ensembles, even being the same molecule ( different starting confirmation ), had their atoms in different order . So I simply build a python script to rewrite the ensemble in a same way . Everything went right but once I performed the PCA I obtain " wrong " result . Looking at both ensembles separately in vmd they are fine , the rewrite ensemble is not broken but if I combined the ensemble they don't " like each other " like if they weren't the same molecule so don't have the same topology , I don't know if it clear . Does anyone had to deal with that ? Regards, Nawel -- Nawel Mele, PhD Research Student Jonathan W Essex Group, School of Chemistry University of Southampton, Highfield Southampton, SO17 1BJ -- 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.
