Alif M Latif a écrit :
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
You don't have enough memory available.
See the command: ulimit -a
You can try also to use the double version of the program (genbox_d
instead of genbox), allocate swap on the machine (man mkswap), or use a
computer having more memory to create your input file.
Cheers,
Stéphane
--
Stéphane Téletchéa, PhD. http://www.steletch.org
Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig
INRA, Domaine de Vilvert Tél : (33) 134 652 891
78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901
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