On 6/19/12 9:34 AM, delara aghaie wrote:
----- Forwarded Message -----
*From:* delara aghaie <[email protected]>
*To:* Discussion list for GROMACS users <[email protected]>
*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
--
========================================
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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