[gmx-users] Regarding g_sgangle index file

[Venkat Reddy]

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.murtola at gmail.com>wrote:

> Hello,
>
> On Sun, Sep 15, 2013 at 5:05 PM, Venkat Reddy <venkat4bt at 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
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-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036