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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