gcc-4.0.2 seems ok for gmx-3.3.1 I have also submitted in bugzilla a similar problem with g_rdf
Regards andrea Sampo Karkola wrote: > Hi, > > the same one, gcc-4.1. Have you tried with other versions? > > Sampo > > andrea spitaleri wrote: >> Hi >> which gcc have you used for compiling gromacs? I have the same problem >> in one pc in which I have >> build gromacs using gcc-4.1 >> >> Regards >> >> andrea >> >> Sampo Karkola wrote: >>> Dear list, >>> >>> the genion program gets halted when I'm trying to replace the solvent >>> molecules with ions. The command >>> >>> genion -s protein_in_waterbox.tpr -o protein_out.gro -p topology.top >>> -pname NA+ -nname CL- -random -neutral -conc 0.1 >>> >>> asks for the group of solvent molecules and when I tell him to use it I >>> get this output >>> >>> Selected 12: 'SOL' >>> Number of (3-atomic) solvent molecules: 9918 >>> >>> Processing topology >>> Replacing 9875 solute molecules in topology file (fdt.top) by 22 NA+ >>> and 21 CL- ions. >>> >>> Back Off! I just backed up fdt.top to ./#fdt.top.2# >>> Replacing solvent molecule 1163 (atom 6250) with NA+ >>> >>> and then nothing happens. genion.log gets generated only half way. My >>> system is Ubuntu 6.10 on AMD AthlonX2 and I've tried the packages via >>> synaptic and also built from source. The same thing happens in both of >>> them. Gromacs version is 3.3.1. However, when I try the same thing on >>> another machine, a HP Proliant ML350 with Debian Sarge and Gromacs >>> 3.3.1, everything goes well. >>> >>> None of the gromacs programs gives any errors before genion. >>> >>> I'll give you more info about the system configuration if anyone asks :) >>> >>> Sampo >>> _______________________________________________ >>> 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 >>> >> > _______________________________________________ > 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 > -- ------------------------------- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ ------------------------------- ******************************************************************** Sostieni la ricerca del San Raffaele con il 5permille! E' SEMPLICE E NON COSTA NULLA. Basta indicare nell'apposito riquadro della dichiarazione dei redditi ("Ricerca sanitaria") il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor: 03 06 42 80 153 e ricordarsi di firmare. Se vuoi saperne di piu' scrivi a [EMAIL PROTECTED] o vai sul sito www.5xmille.org _______________________________________________ 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
