Hi Jio, No, the 'extreme structures' are filtered along the eigenvector and are not real structures. But you wanted the corresponding all-atom ones.
Cheers, Tsjerk On May 12, 2015 00:45, "gromacs query" <gromacsqu...@gmail.com> wrote: > Hi Tsjerk > > In -proj plot of v1 vs Time I used extreme values of V1 and saw structures > on those times. When I compare these structures to the structures obtained > from -extr the atomic positions (of 'same' extremes) are not 'exactly' > matching even after fitting. I tried with double precision as well. > > Am not sure why they are not exactly fitting (trjconv_d -fit). Its like if > I try to fit same structures they should exactly overlap. May the fitting > algorithm has a glitch when molecule is big as in my case (~ 500 atoms) > > > Thanks > Jio > > On Mon, May 11, 2015 at 10:08 PM, Tsjerk Wassenaar <tsje...@gmail.com> > wrote: > > > Hi Jio, > > > > You'll have to look at the projections (-proj), and see at which time > these > > have an extreme value. > > > > Cheers, > > > > Tsjerk > > > > On Mon, May 11, 2015 at 11:00 PM, gromacs query <gromacsqu...@gmail.com> > > wrote: > > > > > Hi Tsjerk > > > > > > Thanks for reply. > > > > > > >> So you can use the times > > > I am unable to use it as explained below. > > > > > > I get extremes output pdb like this: > > > > > > g_covar -s avg.pdb -f all_frames.pdb > > > g_anaeig -s avg.pdb -extr two_extremes.pdb -first 1 -last 1 -nframes 2 > > > > > > > > > Visually two structures in two_extremes.pdb looks fine and expected as > > well > > > but the times mentioned in two_extremes.pdb are MODEL 0 t =0 and > MODEL > > 1 > > > t =1 which seems not correct. In my case t = * should be a frame number > > as > > > I am not using .tpr file and frames are fed as pdb file in which MODEL > 0 > > to > > > n is each frame. > > > > > > Thanks > > > > > > On Mon, May 11, 2015 at 9:47 PM, Tsjerk Wassenaar <tsje...@gmail.com> > > > wrote: > > > > > > > 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. > > > > > > > -- > > > 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. > > > -- > 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. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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