[gmx-users] problem in g_rdf using only x and y
Rebeca García Fandiño
regafan at hotmail.com
Wed Feb 24 16:53:04 CET 2010
Thank you very much.
One question, how should I use it? Should I compile Gromacs again?
Cheers,
Rebeca.
From: gmx3 at hotmail.com
To: jalemkul at vt.edu; gmx-users at gromacs.org
Subject: RE: [gmx-users] problem in g_rdf using only x and y
Date: Wed, 24 Feb 2010 15:29:49 +0100
CC:
Hi,
I realize now that I committed a fix for this bug 3 days after the release
of 4.0.7 (and not 3 days before the release as I initially thought).
If you need it right now, I put the fixed source at:
http://hess.cbr.su.se/~hess/gmx_rdf.c
Berk
> Date: Wed, 24 Feb 2010 06:52:57 -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
>
>
>
> 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
>
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