[gmx-users] genion halted

Sampo Karkola sampo.karkola at helsinki.fi
Thu Mar 29 13:02:49 CEST 2007

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 :)


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