[gmx-users] Re: genbox Not enough memory

Jochen Hub jhub at gwdg.de
Thu Oct 11 14:03:16 CEST 2012

ps: There is a fix for this issue in Gerrit code review:


which introduces a fix genbox -allpair. This avoid the memory-leaky 
neighbor searching, which is the reason for your problem.


Am 10/11/12 10:56 AM, schrieb Jochen Hub:
> Hi,
> this is due to the way genbox -ci is currently implemented. It calles
> add_conf() too often which leaks memory. So you'll have to edit the code.
> Jochen
> You'll have to edit the genbox code in order
> Am 10/10/12 7:14 PM, schrieb Dr. Vitaly Chaban:
>>> Thanks..You are right...The last line of gro file says 250 so it is
>>> in nm!...
>>> On 10 October 2012 12:30, Christopher Neale
>>> <chris.neale at mail.utoronto.ca> wrote:
>>>> Sounds like you ran out of memory. Many clusters have a few
>>>> large-memory nodes. Can you use one of those?
>>>> It's failing on a call for 1.3 Gb of memory, which by itself isn't
>>>> really a lot...
>>>> Also, can you confirm 250 A box length, not 250 nm box length?
>>>> Gromacs defines length in units of nm.
>>>> Chris.
>>>> -- original message --
>>>> I am trying to build a polymer in solvent system by solvating my fully
>>>> extended polymer chains in a box of size 250 250 250 A. I am adding
>>>> 4500 solvent molecules as below
>>>>   genbox -cp Solute.gro -ci solvent.gro -o solvated.gro -nmol 4500
>>>> Adding solvents is a slow process and takes much time and at the end
>>>> I get:
>>>> Program genbox, VERSION 4.5.4
>>>> Source code file: smalloc.c, line: 214
>>>> Fatal error:
>>>> Not enough memory. Failed to realloc 1338273212 bytes for grid->nra,
>>>> grid->nra=0x0
>>>> (called from file nsgrid.c, line 483)
>>>> For more information and tips for troubleshooting, please check the
>>>> website at http://www.gromacs.org/Documentation/Errors
>>>> Is this happening because of the huge amount of free space to be
>>>> filled with the solvent? Please help me.
>> Genbox sometimes suffers from the out-of-memory error. Based on my own
>> investigation, this is indeed what happens here, because the utility
>> uses a kind of grid during its operation. The larger the cell, the
>> more hungry it becomes, no matter how many molecules you want to
>> insert. The standard advice therefore applies - add memory...
>> Another question is why you need such a huge box? The only thing I
>> could imaging is simulating a droplet-vapor/air interface...
>> Another advice is to start with a smaller box and then extend its
>> deminsions using editconf (which does not "care about the box size").
>> Dr. Vitaly V. Chaban
>> MEMPHYS - Center for Biomembrane Physics
>> Department of Physics, Chemistry and Pharmacy
>> University of Southern Denmark
>> Campusvej 55, 5230 Odense M, Denmark

Dr. Jochen Hub
Computational Molecular Biophysics Group
Institute for Microbiology and Genetics
Georg-August-University of Göttingen
Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
Phone: +49-551-39-14189

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