[gmx-users] genbox Not enough memory

Christopher Neale chris.neale at mail.utoronto.ca
Wed Oct 10 18:30:38 CEST 2012

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.


-- 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,
(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.

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