Fw: [gmx-users] segmentation fault-g_spatial
d_aghaie at yahoo.com
Tue Jun 19 15:34:15 CEST 2012
----- 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 [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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