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

[Kester Wong]

Hi Teemu and all, 

Thank you for your reply email. 

보낸사람 : Teemu Murtola <teemu.murt...@gmail.com>
받는사람 : Discussion list for GROMACS us <gmx-us...@gromacs.org>
받은날짜 : 2015년 1월 2일(금) 01:15:25
제목 : Re: [gmx-users] g_select syntax unavailable in GROMACS 5.0 and 5.0.1

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 command "gmx_mpi help selections" did show the available subtopics, however I find this paragraph confusing:

To get started with selections, run, e.g., gmx_mpi select without specifying

selections on the command-line and use the interactive prompt to try out

different selections. This tool provides output options that allow one to see

what is actually selected by the given selections, and the interactive prompt

reports syntax errors immediately, allowing one to try again. The subtopics

listed below give more details on different aspects of selections.

Although the paragraph above mentioened "gmx_mpi select without specifying selections", I had to use "gmx_mpi help selections positions" to be able to see the thread "SPECIFYING POSITIONS IN 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).

Yep, I see. I can understand how this could be counter-intuitive. I got a little confused too, using g_select -h and gmx help selections.

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"?

Yep, this worked for my systems. I suppose this binning method has already taken into account the center of mass of the water droplet?
How do I go from here, to producing the water density profile as a function of z-direction?


Best regards,
Kester

Best regards,
Teemu
On Jan 1, 2015 5:49 AM, "Kester Wong"  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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