[gmx-users] all-atom pca

[Tsjerk Wassenaar]

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.