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:
> 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
> 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
> 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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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