[gmx-users] PCA problems

[jkrieger at mrc-lmb.cam.ac.uk]

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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