[gmx-users] all-atom pca

[gromacs query]

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.
>