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: [email protected]
> To: [email protected]
> 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: [email protected]
> > To: [email protected]
> > 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: [email protected]
> > To: [email protected]
> > 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
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