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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