[gmx-users] Regarding g_sgangle index file

[Teemu Murtola]

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