[gmx-users] genion - hangs up

Rigden, LucianeVMello Luciane.Rigden at liverpool.ac.uk
Thu Jul 26 14:21:46 CEST 2007

Hi Tsjerk

Thanks for the mail.  I think my machine got the problematic Gromacs version when it underwent a big upgrade since I never manually compiled Gromacs on it.  In other words it looks like it got a problematic rpm(/deb etc) via Synaptic(/whatever).  Is that possible - can this problem have fed through somewhere into prebuilt rpms/debs?

I have managed to rectify the problem by using two rpms off the Gromacs website to first downgrade then upgrade again

alien --scripts -i gromacs-3.2.1-1.i386.rpm    
alien --scripts -i gromacs-3.3-1.i386.rpm         

There were a couple of small errors/warnings but the system seems functional.

Synaptic on another machine is suggesting an upgrade from 3.3-1 to 3.3.1-1.  Is that safe to do?

Thanks again for the help


Dr Luciane Vieira de Mello                
School of Biological Sciences		  
Room 2.20, Life Science Building
Tel:(+44) 151 795 5140
FAX:(+44) 151 794 5130
University of Liverpool
Crown St.,Liverpool L69 7ZB, U.K.

-----Original Message-----
From: gmx-users-bounces at gromacs.org on behalf of Tsjerk Wassenaar
Sent: Thu 7/19/2007 7:53 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] genion - hangs up
Hi Luciane,

>  David van der Spoel has replied saying:
>  there is a problem compiling gromacs using gcc 4.x that may cause this. see
> a recent bugzilla entry about it.

Did you compile using the 4.x gcc? In that case, recompile with an
older version (3.x). That solution was suggested in the same

>  While using genion with -np 3, i get 2 lines of Replacing sol. xxx with Na
> and it hangs up. With -np 1 it works fine and replaces 1 SOL with Na. I
> thought it might be my system, so went to /tutor/speptide, but it was the
> same behaviour. I am using gromacs 3.3.1. As I recall genion worked fine
> under 3.2.

I've had this problem, but only with very high salinity. My solution
to that problem (decreasing the allowed minimal distance between ions)
is likely not going to work for you.v So I'd try recompiling if indeed
you used the 4.x gcc version.

>  I am wondering if this problem has already been fixed for version 3.3.1 and
> if a update for that is available.
>  Is the only solution go back to 3.2?

Frankly, we'd say the problem is with gcc, not with gromacs :) The gcc
team should really fix what they've broken in the 4.x series :p



Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
gmx-users mailing list    gmx-users at gromacs.org
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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20070726/c3e1b9c4/attachment.html>

More information about the gromacs.org_gmx-users mailing list