The g_order tool requires a unique sort of index group. There's lots of discussion about it documented in the list archives. In short, you need to use make_ndx to generate an index file that contains _only_ groups pertaining to the carbon atoms you want to analyze, separated by chain (i.e., sn1.ndx/sn2.ndx). Each atom type should be in a separate group.
-Justin Quoting ªL´µ½ <[EMAIL PROTECTED]>: > Hello, gmx developer and users: > > After modifying the source code of g_order in GROMACS 3.3.1 with Bug > #84 and compiling again, I got the error message when using g_order to > calculate order parameteters of POPC bilayer. > The error message is : grp 1 does not have same number of elements as > grp1. > Command line about generating .ndx file and using g_order are listed > below : > > make_ndx -f XXX.pdb -o index.ndx (XXX.pdb is the original > structure of the system) (I chose system or POP as my index group) > > g_order -f YYY.pdb -n index.ndx -s ZZZ.tpr -o -od > > > It will be gotten the same error message when using GROMACS 3.3.2 > version. > > Is something wrong in my process ? > > Thank you. ====================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://bevanlab.biochem.vt.edu/Pages/Personal/justin/ ====================== _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php