[gmx-users] principal component analysis chain break

[胡杰]

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