[gmx-users] Covariance analysis of X-ray ensemble

[Tsjerk Wassenaar]

Hi James,

The default is non-mass weighted. If you want to relate the principal
components to normal modes, and want to obtain mode frequencies, you
(formally) need to include the masses.

Cheers,

Tsjerk

On Fri, Jan 11, 2013 at 7:46 PM, James Starlight <jmsstarlight at gmail.com>wrote:

> Tsjerk, thanks for suggestion!
>
> By the way I've found in the pca.log ( that time pca was done on
> trajectory as well as TRP ( not pdb) files as the inputs ):
>
> Read 30 frames from cam_xray_coors_bb.pdb (time 1 to 30 ps)
> Read reference structure for fit from x_ray.tpr
>
> Analysis group is 'System' (575 atoms)
> Fit group is 'System' (575 atoms)
> Analysis is non-mass weighted
> Fit is non-mass weighted
> Diagonalized the 1725x1725 covariance matrix
> Trace of the covariance matrix before diagonalizing: 350.847
> Trace of the covariance matrix after diagonalizing: 350.847
>
> Wrote 1725 eigenvalues to PCA_eigenval.xvg
> Wrote reference structure to PCA_eigenvec.trr
> Wrote average structure to PCA_average.pdb and PCA_eigenvec.trr
> Wrote eigenvectors 1 to 29 to PCA_eigenvec.trr
>
> It seems that cov.analysis was done also as  non-mass weighted.
> Actualy I extract eigenvectors for further essential dynamics sampling
> runs. In the literature I've found that for EDA eigenvectors from only
> non-mass weighted PCA are suitable. So if its true in what cases mass
> weighted eigenvectors might be used?
>
> James
>
> 2013/1/11 Tsjerk Wassenaar <tsjerkw at gmail.com>:
> > Hi James,
> >
> > You don't need a .tpr file. A .gro or .pdb file will do as well. Unless
> you
> > insist on doing mass-weighted PCA.
> >
> > Cheers,
> >
> > Tsjerk
> >
> > On Fri, Jan 11, 2013 at 4:04 PM, James Starlight <jmsstarlight at gmail.com
> >wrote:
> >
> >> Dear Gromacs users!
> >>
> >>
> >> I want to perform Covariance analysis of my x-ray data sets via
> >>
> >> g_covar -f trr.pdb -s x_ray.tpr -n index -o PCA_eigenval.xvg -v
> >> PCA_eigenvec.trr
> >>
> >> where trr.pdb is the trajectory made from the 30 x-ray structures
> >> (only c-alpha atoms were selected. How I could obtain x_ray.tpr file
> >> for such analysis?
> >>
> >> I've tried to use tpr from full atomic model of the same protein which
> >> I';ve simulated recently. For that p[rotein tpr file have been already
> >> created.  From that model via make_ndx I've defined only backbone
> >> atoms corresponded to the atoms in my pdb ensemble. On the next step
> >> I've used tpbconv on protein.tpr with index file to make reduced tpr
> >> file with atoms corresponded to the backbone of the pdb-ensemble. Now
> >> when I run g_covar with my ensemble and reduced tpr file I obtain
> >> error
> >> *** glibc detected *** g_covar: malloc(): memory corruption:
> >> 0x00007f27df53e018 ***
> >>
> >>
> >> On other hand if I specify for g_covar full-atomic tpr file with the
> >> index ( where atoms corresponded to the trr.pdb are mentioned)
> >>
> >> g_covar -f trr.pdb -s protein.tpr -n index -o PCA_eigenval.xvg -v
> >> PCA_eigenvec.trr
> >>
> >> I obtain another error
> >>
> >> Calculating the average structure ...
> >> Reading frame       0 time    1.000
> >> WARNING: number of atoms in tpx (575) and trajectory (575) do not match
> >>
> >> -------------------------------------------------------
> >> Program g_covar, VERSION 4.5.5
> >> Source code file: /tmp/build/gromacs-4.5.5/src/gmxlib/mshift.c, line:
> 102
> >>
> >> Fatal error:
> >> Molecule in topology has atom numbers below and above natoms (575).
> >> You are probably trying to use a trajectory which does not match the
> >> first 575 atoms of the run input file.
> >>
> >>
> >>
> >> What I've done wrong and how I can define tpr file for trajectory made
> >> from several pdb files ?
> >>
> >>
> >> Thanks for help
> >>
> >> James
> >> --
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> >
> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> >
> > post-doctoral researcher
> > Biocomputing Group
> > Department of Biological Sciences
> > 2500 University Drive NW
> > Calgary, AB T2N 1N4
> > Canada
> > --
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4
Canada