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You could start by reading the gromacs manual, <br>
Section 8.9<br>
On 12/20/11 9:30 AM, yp sun wrote:
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<div>Dear Sir, </div>
<div> </div>
<div>When I run g_rms -s md.tpr -f md.trr -o rmsd.xvg, the
program requires me selecting a group twice as
following: </div>
<div> </div>
<div>g_rms -s md.tpr -f md.trr -o rmsd.xvg后, <span
class="t_tag" href="tag.php?name=%B3%CC%D0%F2">程序</span>两
次要求选<span class="t_tag" href="tag.php?name=%BD%E1%B9%B9">结
构</span>组,如下: </div>
<div>Reading file md.tpr, VERSION 3.3.1 (single precision)<br>
Reading file md.tpr, VERSION 3.3.1 (single precision)<br>
Select group for least squares fit<br>
Opening library file
/home/gromacs-3.3.1/share/gromacs/top/aminoacids.dat<br>
Group 0 ( System) has 519889 elements<br>
Group 1 ( Protein) has 24649 elements<br>
Group 2 ( Protein-H) has 12688 elements<br>
Group 3 ( C-alpha) has 1540 elements<br>
Group 4 ( Backbone) has 4620 elements<br>
Group 5 ( MainChain) has 6172 elements<br>
Group 6 (MainChain+Cb) has 7620 elements<br>
Group 7 ( MainChain+H) has 7668 elements<br>
Group 8 ( SideChain) has 16981 elements<br>
Group 9 ( SideChain-H) has 6516 elements<br>
Group 10 ( Prot-Masses) has 24649 elements<br>
Group 11 ( Non-Protein) has 495240 elements<br>
Group 12 ( SOL) has 495240 elements<br>
Group 13 ( Other) has 495240 elements<br>
Select a group: 1<br>
Selected 1: 'Protein'<br>
Select group for RMSD calculation<br>
Opening library file
/home/gromacs-3.3.1/share/gromacs/top/aminoacids.dat<br>
Group 0 ( System) has 519889 elements<br>
Group 1 ( Protein) has 24649 elements<br>
Group 2 ( Protein-H) has 12688 elements<br>
Group 3 ( C-alpha) has 1540 elements<br>
Group 4 ( Backbone) has 4620 elements<br>
Group 5 ( MainChain) has 6172 elements<br>
Group 6 (MainChain+Cb) has 7620 elements<br>
Group 7 ( MainChain+H) has 7668 elements<br>
Group 8 ( SideChain) has 16981 elements<br>
Group 9 ( SideChain-H) has 6516 elements<br>
Group 10 ( Prot-Masses) has 24649 elements<br>
Group 11 ( Non-Protein) has 495240 elements<br>
Group 12 ( SOL) has 495240 elements<br>
Group 13 ( Other) has 495240 elements<br>
Select a group: 3<br>
Selected 3: 'C-alpha'<br>
trn version: GMX_trn_file (single precision)<br>
Last frame 100 time 100.000<br>
</div>
<div>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.</div>
<div> </div>
<div>Best regards!<br>
<br>
Yeping Sun<br>
CAS Key Laboratory of Pathogenic Microbiology &
Immunology<br>
INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES <br>
NO.1 Beichen West Road,Chaoyang District,Beijing
100101,china</div>
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<pre class="moz-signature" cols="72">--
Gianluca Santoni,
Structural Protein Dynamics Research Team
Institut de Biologie Structurale
41 rue Jules Horowitz
38027 Grenoble Cedex 1
France
_________________________________________________________
Please avoid sending me Word or PowerPoint attachments.
See <a class="moz-txt-link-freetext" href="http://www.gnu.org/philosophy/no-word-attachments.html">http://www.gnu.org/philosophy/no-word-attachments.html</a></pre>
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