[gmx-users] genion halted
spitaleri.andrea at hsr.it
Thu Mar 29 13:16:30 CEST 2007
gcc-4.0.2 seems ok for gmx-3.3.1
I have also submitted in bugzilla a similar problem with g_rdf
Sampo Karkola wrote:
> the same one, gcc-4.1. Have you tried with other versions?
> andrea spitaleri wrote:
>> 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
>> 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 :)
>>> gmx-users mailing list gmx-users at gromacs.org
>>> Please search the archive at http://www.gromacs.org/search before
>>> 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
> 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
Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
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 5permille at hsr.it o vai sul sito
More information about the gromacs.org_gmx-users