Hi Jio, The scores for all-atom structures will be strongly correlated to those for heavy-atom structures. So you can use the times for the heavy-atom extreme projections to extract all-atom structures.
Cheers, Tsjerk On Mon, May 11, 2015 at 10:32 PM, gromacs query <gromacsqu...@gmail.com> wrote: > Hi All > > I am doing PCA and its working fine if I choose few atoms only (heavy) and > I get extreme pdb file having heavy atoms for, say, eigenvector 1. But I > want to have extremes of all-atom structures, so I thought of doing PCA on > all-atoms but I end up with having Segmentation default error which I think > related to comp memory issue. > I think (please correct me) the extreme structures (heavy atoms) would > belong somewhere in the trajectory file. If I can get frame numbers of > these extremes calculated on heavy atoms then I can use same frame numbers > to dump all-atom structures. But how to get frame numbers for these > extremes? may be RMSD with respect to extremes on heavy atoms. > > Thanks > Jio > -- > 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. > -- Tsjerk A. Wassenaar, Ph.D. -- 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.
