[gmx-users] PCA problems

[Tsjerk Wassenaar]

Hi Teresa,

No, the peptide should not be broken. Did you remove jumps over PBC?
The peptide will probably be severely distorted by filtering, though.

Cheers,

Tsjerk


On Wed, Jun 8, 2016 at 8:49 AM, ingram <ingram at fhi-berlin.mpg.de> wrote:

> 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.