[gmx-users] How to check memoryuse limit?

Alif M Latif prism_dead at yahoo.com
Tue May 22 09:30:51 CEST 2007

Dear GROMACS users,

I'm having problem using genbox while trying to solvate my micelle structure. The program produced error "cannot allocate memory". I checked the mailing list archive, and found that Dr. David once told to check the limit command. I tried to type "limit" but the command was not found. Do I need to move to specific directory to use this command? I'm using OS Kernel: Linux version 2.6.9-34.ELsmp (Red Hat 3.4.5-2). Or Maybe something wrong anywhere else?.. I've include the error message (just in case).

Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat
Opening library file /usr/local/gromacs/share/gromacs/top/vdwradii.dat
Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat
#Entries in atommass.dat: 82 vdwradii.dat: 26 dgsolv.dat: 7
Reading solute configuration
Built with Packmol
Containing 787 atoms in 21 residues
Initialising van der waals distances...
Reading solvent configuration
"216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984"
solvent configuration contains 648 atoms in 216 residues

Initialising van der waals distances...
Will generate new solvent configuration of 54x54x54 boxes
Program genbox, VERSION 3.3
Source code file: smalloc.c, line: 137

Fatal error:
realloc for atoms_solvt->atom (-213500416 bytes, file gmx_genbox.c, line 399, at oms_solvt->atom=0x0x 81f07a0)
"We Don't Bother Anyone" (LIVE)
: Cannot allocate memory

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