[gmx-users] Re: genbox Not enough memory

Juliette N. joojoojooon at gmail.com
Wed Oct 10 22:24:17 CEST 2012

Hi again,

The reason I have this big box is that I have fully extended chains of
the length of ~ 250 nm,. In fact this 250 nm is the minimum size that
I can fit the chain in the box; and I am going to fill this box with
solvent and use NPT to increase the density. So I dont need to fill up
the box with solvent entirely. The total number of atoms would be
around 120 000.

I have access to a certain number of nodes. I am wondering if this
"adding of memory" is merely a hardware issue or there is some other
ways to get around this.?

Thank you for your comments,

On 10 October 2012 13:14, Dr. Vitaly Chaban <vvchaban at gmail.com> wrote:
>> 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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J. N.

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