[gmx-users] genbox Not enough memory
joojoojooon at gmail.com
Wed Oct 10 18:41:08 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.
> -- 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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