[gmx-users] genion halted

[andrea spitaleri]

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
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>>
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-- 
-------------------------------
Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
http://biomolecularnmr.ihsr.dom/
-------------------------------

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