[gmx-users] select groups in g_rms

[Gianluca Santoni]

You could start by reading the gromacs manual,
Section 8.9
On 12/20/11 9:30 AM, yp sun wrote:
> 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?, ??? ????? ??,??:
> 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
>
>
>


-- 
Gianluca Santoni,
Structural Protein Dynamics Research Team
Institut de Biologie Structurale
41 rue Jules Horowitz							
38027 Grenoble Cedex 1						
France	
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