[gmx-users] problem in g_rdf using only x and y

[Justin A. Lemkul]

Berk Hess wrote:
> Well, I fixed a bug with g_rdf -xy before the 4.0.7 release.
> But apparently this fix does not work under all conditions.
> Could one of you file a bugzilla and attach a tpr file and a trajectory,
> preferably with only one or very few frames and write the exact command 
> line?

Filed as bugzilla #399.  I uploaded a .tpr and .gro that reproduce the error; if 
you want an actual (small) trajectory, I can provide that as well.

-Justin

> 
> Thanks,
> 
> Berk
> 
>  > Date: Tue, 23 Feb 2010 13:51:39 -0500
>  > From: jalemkul at vt.edu
>  > To: gmx-users at gromacs.org
>  > Subject: Re: [gmx-users] problem in g_rdf using only x and y
>  >
>  >
>  >
>  > Rebeca García Fandiño wrote:
>  > > Hi,
>  > > thank you very much for your answer. However, I have tried with the
>  > > 4.0.7 version, and the problem continues, and it is just the same. I
>  > > have the trajectory and tpr file obtained with the 4.0.4 version. 
> Do you
>  > > think it cares, or maybe is it another problem?
>  >
>  > I think there is a problem in g_rdf, not a 4.0.4 vs 4.0.7 issue. I 
> was actually
>  > about to report this problem, myself. I have simulations that I did with
>  > version 4.0.7, and the RDF analysis hung the exact same way as you 
> reported.
>  >
>  > -Justin
>  >
>  > > Cheers,
>  > > Rebeca.
>  > >
>  > > 
> ------------------------------------------------------------------------
>  > > From: gmx3 at hotmail.com
>  > > To: gmx-users at gromacs.org
>  > > Subject: RE: [gmx-users] problem in g_rdf using only x and y
>  > > Date: Tue, 23 Feb 2010 16:47:43 +0100
>  > >
>  > > Hi,
>  > >
>  > > I fixed this bug in 4.0.7.
>  > >
>  > > Berk
>  > >
>  > > 
> ------------------------------------------------------------------------
>  > > From: regafan at hotmail.com
>  > > To: gmx-users at gromacs.org
>  > > Date: Tue, 23 Feb 2010 15:40:07 +0000
>  > > Subject: [gmx-users] problem in g_rdf using only x and y
>  > >
>  > > Hi,
>  > > I am trying to calculate g_rdf using only the x and y components of 
> the
>  > > distance (gromacs 4.0.4):
>  > >
>  > > g_rdf -f trajectory.xtc -s production1.tpr -n index.ndx -o 
> rdf_Na_xy.xvg
>  > > -com -norm -pbc -xy and the calculations stays at the window:
>  > >
>  > > Select a group: 1
>  > > Selected 1: 'UNK'
>  > > Select a group: 4
>  > > Selected 4: 'Na'
>  > > Reading frame 0 time 0.000
>  > >
>  > > for days...(I had to kill it after 4 days).
>  > >
>  > > Using the same order without -xy takes only 10 minutes.
>  > >
>  > > Is there anything wrong with the commands I am using? Or maybe is 
> there
>  > > a bug in the -xy option?
>  > >
>  > > Thank you very much for your help, in advance.
>  > >
>  > > Best wishes,
>  > >
>  > > Rebeca Garcia.
>  > > <http://serviciosmoviles.es.msn.com/hotmail/movistar.aspx>
>  > > 
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>  >
>  > --
>  > ========================================
>  >
>  > Justin A. Lemkul
>  > Ph.D. Candidate
>  > ICTAS Doctoral Scholar
>  > MILES-IGERT Trainee
>  > Department of Biochemistry
>  > Virginia Tech
>  > Blacksburg, VA
>  > jalemkul[at]vt.edu | (540) 231-9080
>  > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>  >
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================