[gmx-users] strange RMSD output

[Albert]

Hello:

  I've got several individual .pdb file and I use the following command to merge it input .xtc and calculate the rmsd by g_rms:


trjcat -cat -keeplast -f *.pdb -o out.xtc

g_rms -f out.xtc -s 001.pdb -o rmsd.xvg

However, I find a problem with the results. Since most part of each PDB
file overlapped very well only a small loop is different. I first
calculate the rmsd of backbone and got:

@ subtitle "Backbone after lsq fit to Backbone"
     0.0000000    0.0000003
     0.0000000    0.3306260
     0.0000000    0.2545602
     0.0000000    0.3293277
     0.0000000    0.2299789
     0.0000000    0.3216407

Then I calculate the loop region and got:

@ subtitle "Backbone_&_r_120-131 after lsq fit to Backbone"
     0.0000000    0.0000003
     0.0000000    0.1526730
     0.0000000    0.1202507
     0.0000000    0.1449232
     0.0000000    0.1318949
     0.0000000    0.1675032

As we can see, the rmsd of loop region is smaller than the backbone
which I think it should be reversed.......

thank you very much.