<DIV>you need to define a new .ndx which include the no. for the atoms. feed this .ndx file to g_mindist or g_bond with -n option.</DIV>
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<DIV>Yang Ye</DIV>
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<DIV><B><I>Rahul Karyappa <r.karyappa@ncl.res.in></I></B> wrote:</DIV>
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<FONT size=2>Dear all, <BR> I want to know the end-to-end distance of my chain which is surrounded by ions and water molecules. I used g_mindist command to get the values. But I am confused while selecting the groups. The following window occurs:<BR><BR>How many other groups do you want (>= 1) ?<BR>1<BR>Reading file topol.tpr, VERSION 3.2.1 (single precision)<BR>Reading file topol.tpr, VERSION 3.2.1 (single precision)<BR>Opening library file /usr/local/gromacs/share/top/aminoacids.dat<BR>Group 0 ( System) has 9369 elements<BR>Group 1 ( Protein) has 288 elements<BR>Group 2 ( Protein-H) has 288 elements<BR>Group 3 ( C-alpha) has 0 elements<BR>Group 4 ( Backbone)
has 0 elements<BR>Group 5 ( MainChain) has 0 elements<BR>Group 6 (MainChain+Cb) has 0 elements<BR>Group 7 ( MainChain+H) has 0 elements<BR>Group 8 ( SideChain) has 288 elements<BR>Group 9 ( SideChain-H) has 288 elements<BR>Group 10 ( Prot-Masses) has 288 elements<BR>Group 11 ( Non-Protein) has 9081 elements<BR>Group 12 ( SOL) has 9081 elements<BR>Group 13 ( Other) has 9081 elements</FONT></P>
<P><BR><BR>But how to choose the groups?<BR>Waiting for your kind reply.<BR><BR>Rahul Karyappa<BR>NCL, Pune<BR></P>
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