[gmx-users] segmentation fault-g_spatial

delara aghaie d_aghaie at yahoo.com
Tue Jun 19 09:34:04 CEST 2012

Dear Gromacs users. 

I have a protein in a box of water. I want to calculate the SDF of water molecules around the protein. I have used the procedure described in this page:


after two times using trjconv for putting the protein in the center of box and removing its rotation and translation, I use the g_spatial order.

g_spatial -s  ~.tpr -f   ~.xtc   (this is the output .xtc after tao times running trjcov).

I get this message:

Reading frame       7 time   14.000   There was an item outside of the allocated memory. Increase the value given with the -nab option.
Memory was allocated for [-0.374000,-0.301000,-0.217000]        to      [7.676000,7.749000,7.833000]
Memory was required for [-0.375000,6.700000,6.815001]

1) I want to know what exactly does (nab) option?

2) I have changed this -nab value from 4 to 6,8,10,.....40
but again I get something like the mentioned message or the segmentation fault.

What should I do to fix it and is it a limiting value for nab option?

3) Also please let me know, is it possible to calculate SDF of water molecules around a specific residue by creating and index group which contains that residue?

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