[gmx-users] automate gmx sasa

[Andrei Neamtu]

Hello!

Many thanks Teemu!

Andrei

On Sat, Oct 3, 2015 at 9:14 AM, Teemu Murtola <teemu.murtola at gmail.com>
wrote:

> Hi,
>
> On Sat, Oct 3, 2015 at 8:18 AM Andrei Neamtu <neamtuandrei at gmail.com>
> wrote:
>
> > In previous versions if one wants to provide in a script an automatic
> >
> > echo 'two indexes' | g_sas .....
> >
> > it was fairly easy
> >
> > In version 5 gmx sasa expects EOF (Ctrl D) character to end up the
> > selection.
> >
> > How can one provide automatic selection of index groups in version 5?
> > probably it is a basic Bash question but I am stucked in here for several
> > hours! :)
>
>
> It is even easier in Gromacs 5; there is no need for the echo at all. ;) If
> you want to select groups 0 and 1, you can just use
>
>   gmx sasa -surface 0 -output 1 ...
>
> And the same works for arbitrary selections; you just need to be careful
> with quoting. See
>
>   gmx help selections cmdline
>
> for all the alternatives, including how to read more complex selections
> from a file.
>
> Best regards,
> Teemu
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