[gmx-users] index file and freezegrps

Jamie Seyed jamie.seyed at gmail.com
Sun Aug 16 23:29:24 CEST 2009

Dear all,
I have a question about groups in index-file. For making an index file for
freezing some atoms, I used procedure like
http://oldwiki.gromacs.org/index.php/g_order and I deleted extra groups. I
added freezegrp and freezedim in my em.mdp and I did em step. Then I jumped
to md step (because there is no need for pr step since I freezing atoms),
so I added the same lines in md.mdp and I got an error in grompp
run. Obviously in md.mdp since I have tc_grps I will get this error, since I
need all the groups that are defined in tc_grps in index file, and this will
be always required, right? So what is the meaning of "all programs can
generate default index groups" from man-page?? It seems to me the index file
should contains all groups to prevent any error, not just desired groups...
Please correct me if something is missing or wrong in my procedure or my
conclusion. Many Thanks in Advance/Jamie
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