[gmx-users] genion halted
sampo.karkola at helsinki.fi
Thu Mar 29 13:02:49 CEST 2007
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
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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