[gmx-users] g_select syntax unavailable in GROMACS 5.0 and 5.0.1

[Teemu Murtola]

Hi,

Please check the manual for the version you're using, or preferably for the
latest patch release, in case some things have been improved. The short
section on selections in the manual (can't check the section number right
now) mentions two different ways to access the help, and -select 'help ...'
is not one of them. You can try, e.g., 'gmx help selections'.

The support for help through non-interactive selections like in -select
'help' was removed for 5.0 for a few different reasons. The main one is
that 'gmx help' provides a much more natural way to access the information,
in particular now that there are several different command line options
that accept selections (for example, 'gmx gangle' has two different options
that accept selections, and it's not exactly intuitive that these
would/should also accept requests for generic selection help). It's an
unfortunate coincidence that "help all" is now parsed as a valid selection
(that has the name "help" and selects all atoms).

For your second question, is there something wrong with just extending your
existing selection with an additional clause, for example like this:
"resname SOL and res_com z >= 10 and res_com z < 15"?

Best regards,
Teemu
On Jan 1, 2015 5:49 AM, "Kester Wong" <Kester2014 at ibs.re.kr> wrote:

> Dear all,
>
>
> I have recently posted a question on how generate data that allows me to
> plot a droplet profile as a function of z-direction.
>
>
> https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg08966.html
>
> Knowing that this procedure requires the use of g_select, I am able to
> look up some old posts on gmx-users mail list, however, typing g_select
> -select 'help position' and g_select -select 'help all' simply won't work
> (single quotation used instead of double quatation). I have tried these
> commands on GROMACS (5.0 single and 5.0.1 double precision).
>
>
>
> Also, I have another specific question on binning my water droplet along
> the z-direction:
>
> Firstly, I am only able to use g_select to define the bottom bin for water droplet; could you please advise on indexing the bins from the bottom water layer?
>
> g_select_mpi -f traj_comp.xtc -s topol.tpr -n system.ndx -b 9000 -e 10000 -select 'resname SOL and res_com z < 10' -on output-system.ndx
>
>
> How does one select SOL between z > 10 and z < 15, so on and so forth?
>
>
> Happy New Year,
>
> Kester
>
>
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