Fw: [gmx-users] segmentation fault-g_spatial

[Justin A. Lemkul]

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:

"BUGS:
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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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