Fw: [gmx-users] segmentation fault-g_spatial

Justin A. Lemkul jalemkul at vt.edu
Tue Jun 19 15:39:29 CEST 2012

On 6/19/12 9:34 AM, delara aghaie wrote:
> ----- Forwarded Message -----
> *From:* delara aghaie <d_aghaie at yahoo.com>
> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Sent:* Tuesday, 19 June 2012, 12:04
> *Subject:* [gmx-users] segmentation fault-g_spatial
> 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:
> http://www.gromacs.org/Documentation/Gromacs_Utilities/g_spatial
> 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?

According to g_spatial -h:

When the allocated memory is not large enough, a segmentation fault may
occur. This is usually detected and the program is halted prior to the fault
while displaying a warning message suggesting the use of the -nab (Number of
Additional Bins) option. However, the program does not detect all such
events. If you encounter a segmentation fault, run it again with an increased
-nab value."

> 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?

Maybe try an even larger value.  But since it is a known bug, it may simply be 
that the program needs to be fixed or re-written to work more effectively.

> 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?

Yes, it should be.  Try it and see.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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