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, [email protected] 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 > > ======================================== > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
