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

[Justin A. Lemkul]

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

========================================