[gmx-users] 'not allocate memory'

[saly jackson]

Hi

I think the error is not a reason of less memory of my computer. Because in
a supercomputer I see the hollowing error too.

Genbox could be run if I choose the number of atoms less than 5000.

Thanks

Saly

Try 824box_margin = 0.45 overlap:
Neighborsearching with a cut-off of 0.45
Table routines are used for coulomb: FALSE
Table routines are used for vdw:     FALSE
Cut-off's:   NS: 0.45   Coulomb: 0.45   LJ: 0.45
System total charge: 0.000
Grid: 33 x 33 x 33 cells
nri = 3633, nrj = 8848
Try 825box_margin = 0.45 overlap: success (now 4320 atoms)!
Neighborsearching with a cut-off of 0.45
Table routines are used for coulomb: FALSE
Table routines are used for vdw:     FALSE
Cut-off's:   NS: 0.45   Coulomb: 0.45   LJ: 0.45
System total charge: 0.000
Grid: 33 x 33 x 33 cells
nri = 3638, nrj = 8860
Try 826box_margin = 0.45 overlap: success (now 4326 atoms)!
Neighborsearching with a cut-off of 0.45
Table routines are used for coulomb: FALSE
Table routines are used for vdw:     FALSE
Cut-off's:   NS: 0.45   Coulomb: 0.45   LJ: 0.45
System total charge: 0.000
Grid: 33 x 33 x 33 cells
nri = 3644, nrj = 8872
Try 827box_margin = 0.45 overlap: success (now 4332 atoms)!
Neighborsearching with a cut-off of 0.45
Table routines are used for coulomb: FALSE
Table routines are used for vdw:     FALSE
Cut-off's:   NS: 0.45   Coulomb: 0.45   LJ: 0.45
System total charge: 0.000
Grid: 33 x 33 x 33 cells
nri = 3649, nrj = 8908
Try 829box_margin = 0.45 overlap:
Neighborsearching with a cut-off of 0.45
Table routines are used for coulomb: FALSE
Table routines are used for vdw:     FALSE
Cut-off's:   NS: 0.45   Coulomb: 0.45   LJ: 0.45
System total charge: 0.000

-------------------------------------------------------
Program genbox, VERSION 4.5.4
Source code file: smalloc.c, line: 214

Fatal error:
Not enough memory. Failed to realloc 69408 bytes for nl->gid, nl->gid=0x0
(called from file ns.c, line 104)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

"Act like Prometheus would" (Gogol Bordello)
: Cannot allocate memory
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