<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><div id="yiv1766533448"><p>Hello,</p><p><br></p><p></p><p>this has to do with my personal experience of using Gromacs version 4.0.3. So this is not an official response.</p><br><p>The story:<br></p><p></p><p>While I was trying to run an NVT simulation in a monoclinic box I encountered the following problem:</p><p><br></p><p>Fatal error:<br>25 of the 336080 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (0.895 nm) or the two-body cut-off distance (0.895 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck<br></p><p></p><p></p><br>and the:<br>Not all bonded interactions have been properly assigned to the domain decomposition cells<br><br>Trying to put aside the fact that my system had any bug I found in the net the
following:<br>http://www.gromacs.org/pipermail/gmx-developers/2008-January/002373.html<br><br>In order to overcome this error I increased the value of<br>table-extension = 30<br>in my mdp file in such a way, as to be bigger from my biggest dimension I had in my system. The ran proceeded (until now that I'm writing this e-mail) without any problem.<br><br>This value has to do with the cut-off of pairs1-4 LJ interactions and is calculated in nm.<br><br>JFYI<br>Regards,<br>Nikos<br><br><br><br></div></td></tr></table><br>