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 Luciane 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: [EMAIL PROTECTED] 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 discussion. > 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 Cheers, Tsjerk -- 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@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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