Jamie Seyed wrote:
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
If you specify an index file no automatic generation is done. So you
need to specify all groups that you use in the index file (e.g. Protein,
System etc.).
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David.
________________________________________________________________________
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Dept. of Cell and Molecular Biology, Uppsala University.
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