From: Stéphane Téletchéa <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <[email protected]>
To: Discussion list for GROMACS users <[email protected]>
Subject: Re: [gmx-users] How to check memoryuse limit?
Date: Tue, 22 May 2007 15:09:37 +0200
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.
Using the double version will only makes things worse, since it uses
double the amount of memory.
But are you sure you want to make a box with 30 million water molecules?
Maybe you mixed up Angstroms and nanometers?
Berk.
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