[gmx-users] index file and freezegrps

David van der Spoel spoel at xray.bmc.uu.se
Sun Aug 16 23:44:01 CEST 2009

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 van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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