[gmx-users] normalized overlap
Mark Abraham
mark.j.abraham at gmail.com
Tue Dec 20 06:07:09 CET 2016
Hi,
GROMACS tools write the eigenvalue to the time field of trr files, so both
of your runs are presumably computing the same quantity from the same input
data (which you can check by comparing the .xvg files to the output of gmx
dump on the trr files). I will amend the docs of gmx anaeig to note that
the -eig and -eig2 options permit you to supply eigenvalues, which will
replace those read from the trr file. So, if what you want is to do the
analysis with eigenvalues all zero, then make copies of your .xvg files and
zero the values suitably.
Mark
On Tue, Dec 20, 2016 at 2:45 AM Lovas, Sandor <SandorLovas at creighton.edu>
wrote:
> Hi Mark,
> I suspect this is a bug in the code. I have checked my inputs
> (eigenval.xvg and eigenvector.trr) and they looked OK. I know that the
> first and the second frames in the eigenvector.trr are for the
> reference and average structures, respectively. But in this case I
> think it does not matter what they are, since the eignevalues are not
> zero in the eigenval.xvg filesm, so if they are read from the input or
> used during the calculation they should affect the result.
>
> Here is how I generated the files. Btw, I use gromacs-2016, but
> previous versions have the same problem:
>
> 1. gmx covar -f traj.xtc -s conf.pdb -o eigenval_tot -v eigenvec_tot;
> full trejectory
>
> 2. gmx covar -f traj.xtc -s conf.pdb -e 500000 -o eigenval_5 -v
> eigenvec_5 ; first half of tjhe simulation
>
> 3. gmx anaeig -v eigenvec_5.trr -eig eigenval_5.xvg -v2
> eigenvec_tot.trr -eig2 eigenval_tot.xvg; using the eigenvalues
>
> trr version: GMX_trn_file (single precision)
> Read non mass weighted reference structure with 443 atoms from
> eigenvec_5.trr
> Read non mass weighted average/minimum structure with 443 atoms from
> eigenvec_5.trr
> Read 1329 eigenvectors (for 443 atoms)
>
> Read 1329 eigenvalues from eigenval_5.xvg
> Read non mass weighted reference structure with 443 atoms from
> ../eigenvec_tot.trr
> Read non mass weighted average/minimum structure with 443 atoms from
> ../eigenvec_tot.trr
> Read 1329 eigenvectors (for 443 atoms)
>
> Read 1329 eigenvalues from ../eigenval_tot.xvg
> RMSD (without fit) between the two average structures: 0.093 (nm)
>
> 2 eigenvectors selected for output: 1 1329
> Will compare the covariance matrices using 1329 dimensions
> Trace of the two matrices: 29.8148 and 29.2895
> Square root of the traces: 5.46029 and 5.41198
> The overlap of the covariance matrices:
> normalized: 0.679
> shape: 0.679
>
> 4. gmx anaeig -v eigenvec_5.trr -v2 eigenvec_tot.trr ; no eigenvalues
> are in the input
>
> trr version: GMX_trn_file (single precision)
> Read non mass weighted reference structure with 443 atoms from
> eigenvec_5.trr
> Read non mass weighted average/minimum structure with 443 atoms from
> eigenvec_5.trr
> Read 1329 eigenvectors (for 443 atoms)
>
> Read non mass weighted reference structure with 443 atoms from
> ../eigenvec_tot.trr
> Read non mass weighted average/minimum structure with 443 atoms from
> ../eigenvec_tot.trr
> Read 1329 eigenvectors (for 443 atoms)
>
> RMSD (without fit) between the two average structures: 0.093 (nm)
>
> 2 eigenvectors selected for output: 1 1329
> Will compare the covariance matrices using 1329 dimensions
> Trace of the two matrices: 29.8147 and 29.2895
> Square root of the traces: 5.46029 and 5.41198
> The overlap of the covariance matrices:
> normalized: 0.679
> shape: 0.679
>
>
>
>
> In both cases the normalized value (0.679) are the same.
>
> Sandor
>
>
> >Hi,
> >
> >We don't have anything to go upon... this could be a code bug or a
> usage
> >bug. How did you generate your input file? Have you inspected your
> input
> >file to check for sanity? (e.g. with gmx dump, remembering that the
> first
> >frame or two are different, see gmx covar -h) What is the whole
> terminal
> >>output of both stages?
>
> >Mark
>
> >On Sat, Dec 17, 2016 at 10:30 AM Lovas, Sandor <SandorLovas at
> >creighton.edu>
> wrote:
>
> > I have asked this question a few days back; I try one more time:
> >
> > When I am trying calculate the degrees of overlap of subsets of a
> > simulation to the whole trajectory by following the explanation in
> the
> > manual gmx anaeig:
> > "When -v, -eig, -v2 and -eig2 are given, a single number for the
> > overlap between the covariance matrices is generated...."
> >
> > For me, it does not make any difference whether or not I use the "-
> eig"
> > and "-eig2" inputs, the results for normalized overlap are the same.
> In
> > other words, the normalized overlap is not calculated by using the
> > equation given in the manual:
> >
> > "normalized overlap = 1 - difference/sqrt(tr(M1) + tr(M2))
> > ....
> > where M1 and M2 are the two covariance matrices and tr is the trace
> of
> > a matrix."
> >
> > Sandor
> > --
> > ______________________________________
> > Dr. Sandor Lovas, Professor
> > Department of Biomedical Sciences
> > Creighton University
> > 2500 California Plaza,
> > Omaha, NE 68178, USA
> >
> > Phone: 402-280-5753
> > Fax: 402-280-2690
> >
> >
> > --
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> --
> ______________________________________
> Dr. Sandor Lovas, Professor
> Department of Biomedical Sciences
> Creighton University
> 2500 California Plaza,
> Omaha, NE 68178, USA
>
> Phone: 402-280-5753
> Fax: 402-280-2690
>
>
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