Hello, On Sun, Sep 15, 2013 at 5:05 PM, Venkat Reddy <venkat...@gmail.com> wrote:
> I found g_sgangle is the suitable tool > to calculate the angle between two cholesterol rings. But the problem is, I > want to do this analysis for my whole system, which has 40 cholesterol > molecules. Whereas I can input either two or three atoms in the g_sgangle > index file. A quick surf through the gmx-archive yielded a suggestion like: > > "An index group should contain all (1,2) pairs such that the overall group > size is a multiple of two. The index group has to be in a particular > order, like 1 2 1 2 etc.," > > <clip> > > I got the output index file in the same order.,i.e., R5 R0 R5 R0....etc. > But when I execute g_sgangle, it is saying something wrong with the index > file. How to solve this error? > How to organize the index file in a multiple of 2? > It is only possible to calculate a single angle in one invocation of g_sgangle. You could script your calculation to run g_sgangle once for each of your molecules, but that gets somewhat tedious. With the development version (from the git master branch), you can use a much more powerful 'gmx gangle' tool, which can calculate multiple angles in one go. As an added bonus, you don't need to invoke g_select separately, but can simply provide the selection to the tool. Best regards, Teemu -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
