[gmx-users] select groups in g_rms

[yp sun]

Dear Sir, 
 
When I run g_rms -s md.tpr -f md.trr -o rmsd.xvg, the program requires me selecting a group twice as following: 
 
g_rms -s md.tpr -f md.trr -o rmsd.xvg后, 程序两次要求选结构组,如下: 
Reading file md.tpr, VERSION 3.3.1 (single precision)
Reading file md.tpr, VERSION 3.3.1 (single precision)
Select group for least squares fit
Opening library file /home/gromacs-3.3.1/share/gromacs/top/aminoacids.dat
Group     0 (      System) has 519889 elements
Group     1 (     Protein) has 24649 elements
Group     2 (   Protein-H) has 12688 elements
Group     3 (     C-alpha) has  1540 elements
Group     4 (    Backbone) has  4620 elements
Group     5 (   MainChain) has  6172 elements
Group     6 (MainChain+Cb) has  7620 elements
Group     7 ( MainChain+H) has  7668 elements
Group     8 (   SideChain) has 16981 elements
Group     9 ( SideChain-H) has  6516 elements
Group    10 ( Prot-Masses) has 24649 elements
Group    11 ( Non-Protein) has 495240 elements
Group    12 (         SOL) has 495240 elements
Group    13 (       Other) has 495240 elements
Select a group: 1
Selected 1: 'Protein'
Select group for RMSD calculation
Opening library file /home/gromacs-3.3.1/share/gromacs/top/aminoacids.dat
Group     0 (      System) has 519889 elements
Group     1 (     Protein) has 24649 elements
Group     2 (   Protein-H) has 12688 elements
Group     3 (     C-alpha) has  1540 elements
Group     4 (    Backbone) has  4620 elements
Group     5 (   MainChain) has  6172 elements
Group     6 (MainChain+Cb) has  7620 elements
Group     7 ( MainChain+H) has  7668 elements
Group     8 (   SideChain) has 16981 elements
Group     9 ( SideChain-H) has  6516 elements
Group    10 ( Prot-Masses) has 24649 elements
Group    11 ( Non-Protein) has 495240 elements
Group    12 (         SOL) has 495240 elements
Group    13 (       Other) has 495240 elements
Select a group: 3
Selected 3: 'C-alpha'
trn version: GMX_trn_file (single precision)
Last frame        100 time  100.000

I don't understand how to make the first selction "Select group for least squares fit", and the secend select Select "group for RMSD calculation", and I don't understand the meaning of these selection. I hope you can help me. Thanks.
 
Best regards!

Yeping Sun
CAS Key Laboratory of Pathogenic Microbiology & Immunology
INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES 
NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china
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