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@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
