[gmx-users] principal component analysis chain break

[Tsjerk Wassenaar]

Ni hao Jie,

The extreme projections are typically pretty meaningless. But if you want
them or the more meaningful PCA output, do make sure you remove jumps over
PBC from your input trajectory and have the molecules whole/clustered.

Cheers,

Tsjerk

On Oct 7, 2016 11:21 AM, "胡杰" <hujie14 at mails.ucas.ac.cn> wrote:

> Dear Gromacs community,
>
> It's a question about principal  component analysis(PCA).
> Starting with a tRNA trajectory xtc file and a reference pdb file I use
> the following command, :
> 1. g_covar -s ref_backbone.pdb -f md_backbone.xtc
> 2. g_anaeig -s ref_backbone.pdb -f md1_backbone.xtc -extr extreme1.pdb
> -first 1 -last 1 -nframes 30
>
> extreme1.pdb is what I want, but the chain of the structure break at some
> place showing from PLMOL or VMD. What's the matter. Could you please tell
> me how to get the compelet structure of extreme1.pdb.
>
> best regards
> Jie
>
>
>
>
>
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