[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>
> >  > > 
> > ------------------------------------------------------------------------
> >  > > ¿Quieres tener a tus amigos de Facebook en Messenger? ¡Clic AQUÍ!
> >  > > <http://vivelive.com/feedfacebook/>
> >  > > 
> > ------------------------------------------------------------------------
> >  > > New Windows 7: Find the right PC for you. Learn more.
> >  > > <http://windows.microsoft.com/shop>
> >  > > 
> > ------------------------------------------------------------------------
> >  > > Navega con el navegador más seguro de todos. ¡Descárgatelo ya!
> >  > > <http://www.vivelive.com/internetexplorer8>
> >  > >
> >  >
> >  > --
> >  > ========================================
> >  >
> >  > 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
> >  >
> >  > ========================================
> >  > --
> >  > gmx-users mailing list gmx-users at gromacs.org
> >  > http://lists.gromacs.org/mailman/listinfo/gmx-users
> >  > Please search the archive at http://www.gromacs.org/search before 
> > posting!
> >  > Please don't post (un)subscribe requests to the list. Use the
> >  > www interface or send it to gmx-users-request at gromacs.org.
> >  > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > 
> > ------------------------------------------------------------------------
> > New Windows 7: Find the right PC for you. Learn more. 
> > <http://windows.microsoft.com/shop>
> > 
> 
> -- 
> ========================================
> 
> 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
> 
> ========================================
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
 		 	   		  
New Windows 7: Find the right PC for you. Learn more. 		 	   		  
_________________________________________________________________
Recibe las alertas Hotmail en tu móvil ¡Actívalas ya!
http://home.mobile.live.com/MobileAttach.mvc/?mkt=es-es
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100224/322c2dd0/attachment.html>


More information about the gromacs.org_gmx-users mailing list