[gmx-users] genbox Not enough memory

[Juliette N.]

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.
> --
> Thanks,
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists



-- 
Thanks,
J. N.