[gmx-users] Re: genbox Not enough memory

Dr. Vitaly Chaban vvchaban at gmail.com
Wed Oct 10 19:14:56 CEST 2012

> 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 GROMACS
>> 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

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