[gmx-users] only three options for genrestr

[Justin A. Lemkul]

On 6/20/12 4:52 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
> Hi everybody,
> I wanted to fix the whole protein with "genrestr" so that only the water
> molecules are flexible. I already did this once and there I had about 13
> options what I want to fix so that I could select "protein"
> But now I only have 3 options what I can fix: System, Water, SOL.
> The only difference to the first time I used it is that now there is a
> layer of dummy atoms around my protein simulating the membrane.
> So my question is: How can I now only fix the protein and not the whole
> system.

All Gromacs programs generate default groups based on the contents of the files 
at hand.

http://www.gromacs.org/Documentation/Terminology/Default_Index_Groups

If you're only getting System, Water, and SOL, then the file you've passed to 
genrestr contains only water or you are otherwise overriding the default groups 
by using another index file (which we can't tell because you haven't provided 
your command line).  Check the contents of your files.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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