[gmx-users] all-atom pca

[gromacs query]

Hi Tsjerk

I think am lost now when you say 'filtered' which I don't know what it
means. Manual says:

-proj : calculate projections of a trajectory on eigenvectors

-extr : calculate the two extreme projections along a trajectory on the
average structure

Saying that analysis done on heavy atoms and structures obtained from -extr
(only two) and -proj (max and min) should exactly match. As you said
extremes from -extr will not exactly overlap -proj for heavy atom analysis
as they are not 'real ones' but how they are filtered? (some philosophical
concept would really help as sometime back you explained giving hands
motion on desk!)

There is separate -filt option which I have not used.

Thanks
Jio

On Tue, May 12, 2015 at 5:43 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> 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" <gromacsquery at 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 <tsjerkw at 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 <
> gromacsquery at 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 <tsjerkw at 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 <
> > > gromacsquery at 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-request at 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-request at 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-request at 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-request at 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-request at 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-request at gromacs.org.
>