[gmx-users] PCA problems

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

Thanks Tsjerk,

Isn't the progressive fit supposed to rotate everything back into the same
orientation without having to worry about inferring that orientation from
a reference structure that doesn't align well? Each configuration should
in theory align well to its predecessor all the way back to the starting
structure (which is what I'd usually take as a reference anyway).

The original note I was thinking of says as follows:

'''Before a PCA, all structures should be superimposed onto a common
reference
structure. This can be problematic for very flexible systems such as
peptides,
where the fit may be ambiguous, leading to artificial structural
transitions. In
certain cases, such problems may be alleviated by using a progressive fit,
where
each structure is superimposed onto the previous one. It is also important
to note
that when results of different PCAs are to be compared with each other, then
each individual PCA should be based on the same reference structure used for
superposition.'''

Please could you explain further what it is I have misunderstood.

Also would you say a progressive fit is a bad idea for more structured
proteins?

Many thanks
James

> 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.
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