[gmx-users] can dynamic selection be used with gmx rdf?

[Cardenas, Alfredo E]

Here I am posting the solution of the problem that I described in my first post:

gmx rdf -f ../../../../traj_200to500.xtc -s ../../../../step7_4.tpr  -o -cn -rmax 0.8 -excl -ref '(resname DPPS and name
O22) and within 0.3 of name CAL'  -sel 'name OH2'

Alfredo
________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Cardenas, Alfredo E <alfredo at ices.utexas.edu>
Sent: Thursday, February 28, 2019 10:50 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] can dynamic selection be used with gmx rdf?

Hi Mark,
Thanks for your reply. I have tried the following run:

gmx rdf -f ../../../traj_200to500.xtc -s ../../../step7_4.tpr  -o -cn -rmax 0.8 -excl -ref -sf selection1.dat  -sel -sf selection2.dat

where the selections files are:

selection1.dat:
rdist = name CAL distance from name O22;
name O22 and rdist  <= 0.3;

(for the first line I am following an example in the User guide)

selection2.dat:
name OH2

When attempting to run I get an error:
Error in user input:
Invalid command-line options
  In command-line option -sf
    Error in parsing selections from file 'selection1.dat'
      Invalid selection 'rdist = name CAL distance from name O22'
        syntax error
  In command-line option -sf
    Error in adding selections from file 'selection2.dat'
      Too few selections provided

I guess the syntax of my selection instructions is wrong.
Any help will be appreciated.
Thanks,

Alfredo



________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Mark Abraham <mark.j.abraham at gmail.com>
Sent: Wednesday, February 27, 2019 5:27 PM
To: gmx-users at gromacs.org
Cc: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: Re: [gmx-users] can dynamic selection be used with gmx rdf?

Hi,

One way to check that is to consult the online documentation...
http://manual.gromacs.org/documentation/current/onlinehelp/gmx-rdf.html shows
options taking dynamic selections!

Mark

On Wed, 27 Feb 2019 at 15:08 Cardenas, Alfredo E <alfredo at ices.utexas.edu>
wrote:

> Hello all,
> I would like to calculate the rdf between a set of oxygen atoms in a lipid
> bilayer to water. But I would like to include in this calculation only a
> subset of these oxygen atoms that come closer (< 0.3 nm) to Ca ions. I
> wonder if such a dynamic selection is possible combined with the rdf tool.
> Thanks
> Alfredo Cardenas
>
>
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