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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