[gmx-users] PCA problems

[Tsjerk Wassenaar]

Hi James,

'Spurious alignment' is the dependence of the resulting ensemble on the
reference structure. Unfortunately, that's not solved by a progressive fit.
Rather, in a progressive fit, the same configuration can have multiple
orientations, based on the previous structures, which is also problematic
when you're trying to understand spatial correlations between atoms within
their reference frame.

Cheers,

Tsjerk

On Wed, Jun 8, 2016 at 9:27 AM, <jkrieger at mrc-lmb.cam.ac.uk> wrote:

> Dear Teresa,
>
> That sounds like a periodic boundary issue to me. It could be fixed by
> using a tpr instead of a gro as the gmx covar manual says "All structures
> are fitted to the structure in the structure file. When this is not a run
> input file periodicity will not be taken into account." Alternatively if
> you don't have a tpr you could use gmx trjconv first with -pbc whole or
> -pbc nojump.
>
> I also remember reading (I think it was in the Hayward and de Groot review
> 2008) that fitting peptides to a reference structure can cause spurious
> alignments. I don't know if this is also related to what you're seeing but
> it might be worth using gmx trjconv again with-fit progressive then use
> -nofit in gmx covar.
>
> Best wishes
> James
>
> > Dear GROMACS community
> >
> > I am trying to complete a PCA analysis of my peptide adsorbed to a
> > surface. However when I use :
> >
> > gmx covar -s trajectory.gro  -f md_golp_vacuo.xtc
> >
> > and select the protein for both the least squares fit and covariance
> > calculation, followed by
> >
> >
> > gmx anaeig -s trajectory.gro -f md_golp_vacuo.trr -filt filter1.gro
> > -first 1 -last 1 -skip 100
> >
> > and I select the peptide for the least squares and covariance
> > calculation
> >
> > My peptide is now broken up into pieces. Is this right?
> >
> >
> >
> > Best
> > Teresa
> > --
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-- 
Tsjerk A. Wassenaar, Ph.D.