[gmx-users] genion halted

[andrea spitaleri]

Hi
yes I do use genion and g_rdf properly with 4.0.2

Regards

and

Sampo Karkola wrote:
> Hi,
> 
> so you got genion working with 4.0.2?
> 
> Sampo
> 
> andrea spitaleri wrote:
>> 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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-- 
-------------------------------
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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