[gmx-users] automate gmx sasa

Teemu Murtola teemu.murtola at gmail.com
Sat Oct 3 08:14:43 CEST 2015


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,

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