Dear D.M. I wrote g_spatial and Justin is correct that you simply need to use a larger number for -nab.
It's not a "bug" per se, it is simply that I didn't write the program to do two loops through the input trajectory (one to determine the required bins and then allocate memory and then another loop to count the values). So it is just quick and dirty coding, but when -nab is sufficiently large it will not be wrong. Here is what happens: let's say that you have a cubic box. You then use trjconv to do a fitting in which you rotate the box differently in different frames. Now the length of the new x-axis in a frame could be the length of the diagonal of your box, which is substantially longer. This is why you need to ask the program to allocate memory for additional bins (which will be written out to your cube file, making it larger, so you don't want to set -nab too much larger than is necessary). Pressure coupling also influences this, but not as much. Note that if you make your bins half as large (for higher resolution) then you will need to double the value that you provide to -nab. I usually use -nab 50. You may need a larger value if you use smaller bins or a very rectangular system which you rotate before running through g_spatial. You may also have to use very large values of -nab if you do a fitting on a system where your central group is not centered (use the suggested trjconv preparation listed in g_spatial -h). Finally, if you are using incredibly small bin sizes, then you might really be running into an out-of-memory condition, although that should not result in a segfault as the program should exit cleanly if it can not allocate the required memory. Chris. ---- 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? 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? Thanks Regards D.M -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
