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

Justin A. Lemkul Wed, 24 Feb 2010 07:57:44 -0800


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: g...@hotmail.com
To: jalem...@vt.edu; gmx-users@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: jalem...@vt.edu
 > To: gmx-users@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 atrajectory,> > preferably with only one or very few frames and write the exactcommand

 > > line?
 >

> Filed as bugzilla #399. I uploaded a .tpr and .gro that reproduce theerror; 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: jalem...@vt.edu
 > > > To: gmx-users@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 thesame. 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 Idid with

 > > > version 4.0.7, and the RDF analysis hung the exact same way as you
 > > reported.
 > > >
 > > > -Justin
 > > >
 > > > > Cheers,
 > > > > Rebeca.
 > > > >
 > > > >

> >------------------------------------------------------------------------

 > > > > From: g...@hotmail.com
 > > > > To: gmx-users@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: rega...@hotmail.com
 > > > > To: gmx-users@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 ycomponents 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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