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-boun...@maillist.sys.kth.se
on behalf of Cardenas,
Alfredo E
Sent: Thursday, February 28, 2019 10:50 AM
To: gmx-us...@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-boun...@maillist.sys.kth.se
on behalf of Mark Abraham
Sent: Wednesday, February 27, 2019 5:27 PM
To: gmx-us...@gromacs.org
Cc: gromacs.org_gmx-users@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
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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