Thank you sir for the nice tip. I will try it out and let you know if I have any problem.
On Tue, Sep 17, 2013 at 12:38 AM, Teemu Murtola <teemu.murt...@gmail.com>wrote: > 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 > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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
