Dear Justin Thanks for your reply.
I know, with g_select, I obtain index groups that tell me which atoms satisfy the given criteria and with trjorder, the coordinates of those atoms are reordered such that they are listed in sequence in the new trajectory. But g_select gives an output file (size.xvg) and trjorder gives an output file (nshell.xvg). Both of these output files contain number of atoms satisfy the given criteria. In my case these number are not the same at the special frame. Why?
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