[gmx-users] genion halted

andrea spitaleri spitaleri.andrea at hsr.it
Thu Mar 29 13:07:08 CEST 2007

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 :)
> Sampo
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Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)

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