[gmx-users] all-atom pca

[Tsjerk Wassenaar]

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
> > > > > --
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> > > > --
> > > > Tsjerk A. Wassenaar, Ph.D.
> > > > --
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> > --
> > Tsjerk A. Wassenaar, Ph.D.
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