[gmx-users] PCA problems

jkrieger at mrc-lmb.cam.ac.uk jkrieger at mrc-lmb.cam.ac.uk
Wed Jun 8 09:28:00 CEST 2016


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
> --
> 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.
>



More information about the gromacs.org_gmx-users mailing list