[gmx-users] problem in g_rdf using only x and y
Justin A. Lemkul
jalemkul at vt.edu
Wed Feb 24 16:55:19 CET 2010
Rebeca García Fandiño wrote:
> Thank you very much.
> One question, how should I use it? Should I compile Gromacs again?
Yes. Changes to the source code require re-compilation and installation.
I'll add my thanks to Berk as well :)
-Justin
> 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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--
========================================
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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