[gmx-users] only three options for genrestr

[reisingere at rostlab.informatik.tu-muenchen.de]

Hi Justin,
okey, thanks for your answer. I will try to find out were I overwrite
those groups.
Eva

>
>
> 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
>
> --
> ========================================
>
> 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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