[gmx-users] error during solvation of system

Mark Abraham Mark.Abraham at anu.edu.au
Tue May 5 09:25:56 CEST 2009

nitu sharma wrote:
> Dear all
>               I am doing simulation of membrane protei in lipid bilayer 
> after making complex of protein and lipid bilayer  I was going to step 
> genbox  to  solvate the system but when I was doing this the one error 
> came like this-
> Program genbox, VERSION 4.0.3
> Source code file: smalloc.c, line: 179
> Fatal error:
> Not enough memory. Failed to realloc 1008588692 bytes for nlist->jjnr, 
> nlist->jjnr=0x6e708008
> (called from file ns.c, line 499)
> -----------------------------------------
> "She Needs Cash to Buy Aspirine For Her Pain" (LIVE)
> : Cannot allocate memory
> What is this problem .
> Is it related with system memory on which i am working or it related 
> with gromacs .
> If anybody have idea about this please suggest me something.

Update to 4.0.4. Otherwise, the code has tried to allocate a gigabyte of 
memory, which wasn't available for some reason. Check the sizes of your 
inputs, try another computer system, free up system memory, increase 
system virtual memory.


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