<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><DIV>Dear Sir, </DIV>
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<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>
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<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>
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<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></td></tr></table>