[gmx-users] genion - hangs up

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Jul 19 08:53:43 CEST 2007

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

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