<html><body><div style="color:#000; background-color:#fff; font-family:arial, helvetica, sans-serif;font-size:12pt"><div>Dear Gromacs users. <br></div><div>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:</div><div><br></div><div>http://www.gromacs.org/Documentation/Gromacs_Utilities/g_spatial</div><div><br></div><div>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.</div><div><br></div><div>g_spatial -s ~.tpr -f ~.xtc (this is the output .xtc after tao times running trjcov).</div><div><br></div><div>I get this message:</div><div><br></div><div><span style="color: rgb(0, 0, 127);">Reading frame 7 time 14.000 There was an item outside of the allocated memory. Increase the
value given with the -nab option.</span><br style="color: rgb(0, 0, 127);"><span style="color: rgb(0, 0, 127);">Memory was allocated for [-0.374000,-0.301000,-0.217000] to [7.676000,7.749000,7.833000]</span><br style="color: rgb(0, 0, 127);"><span style="color: rgb(0, 0, 127);">Memory was required for [-0.375000,6.700000,6.815001]</span></div><div><br></div><div>1) I want to know what exactly does (nab) option?</div><div><br></div><div>2) I have changed this -nab value from 4 to 6,8,10,.....40</div><div>but again I get something like the mentioned message or the segmentation fault.</div><div><br></div><div>What should I do to fix it and is it a limiting value for nab option?</div><div><br></div><div>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?<br></div><div><br></div><div><br></div><div>Thanks</div><div>Regards</div><div>D.M<br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div></div></body></html>