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Hi,<br><br>Your solution seems to indicate that your system is unstable.<br>My guess is that your system was not well equilibrated and at some point<br>some non-bonded interactions were at a distance of more than cut-off+tab_ext.<br>That would make your system explode. In that case increasing tab_ext to 2 nm<br>should also suffice.<br><br>Berk<br><br><br><hr id="stopSpelling">Date: Tue, 3 Mar 2009 08:33:52 -0800<br>From: lastexile7gr@yahoo.de<br>To: gmx-users@gromacs.org<br>Subject: [gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3<br><br><table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td style="font-family: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; font-size: inherit; line-height: inherit; font-size-adjust: inherit; font-stretch: inherit;" valign="top"><div id="EC_yiv1766533448">Hello,<BR><br><BR><BR>this has to do with my personal experience of using Gromacs version 4.0.3. So this is not an official response.<BR><br>The story:<br><BR><BR>While I was trying to run an NVT simulation in a monoclinic box I encountered the following problem:<BR><br><BR>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><BR><BR><BR><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></tbody></table><br><br /><hr />See all the ways you can stay connected <a href='http://www.microsoft.com/windows/windowslive/default.aspx' target='_new'>to friends and family</a></body>
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