<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><br></div><div>Dears,</div><div><br></div><div>Following on the issue of long range bonded terms preventing the use of DD and before fixed using PD. </div><div><br></div><div>We have looked into the groupcoord.c solution but are currently stuck. Our idea was to supplement at each step the local atom list of each node with the atoms involved in those long range bonded terms (total of six atoms). We have bypassed the check on the minimum DD box size (15 nm) by forcing the code to take the decomposition we choose. Here 2x2x2. </div><div><br></div><div>Of course now mdrun crashes when getting to calculate those long range bonded interactions and complains that they are missing. The error message is given bellow. We have trouble finding where exactly the code determines which coordinates to communicate to each domain. </div><div><br></div><div>Any suggestion or hint would be greatly appreciated.</div><div><br></div><div>XAvier and Manel.</div><div><br></div><div>…</div><div><span style="font-family: 'courier new', monospace; ">A list of missing interactions:</span><br style="font-family: 'courier new', monospace; "><span style="font-family: 'courier new', monospace; "> Bond of 60636 missing 1</span><br style="font-family: 'courier new', monospace; "><span style="font-family: 'courier new', monospace; "> Improper Dih. of 12 missing 2</span><br style="font-family: 'courier new', monospace; "><br style="font-family: 'courier new', monospace; "><span style="font-family: 'courier new', monospace; ">Molecule type 'rhodimmer'</span><br style="font-family: 'courier new', monospace; "><span style="font-family: 'courier new', monospace; ">the first 10 missing interactions, except for exclusions:</span><br style="font-family: 'courier new', monospace; "><span style="font-family: 'courier new', monospace; "> Improper Dih. atoms 117 423 279 1066 global 117 423 279 1066</span><br style="font-family: 'courier new', monospace; "><span style="font-family: 'courier new', monospace; "> Bond atoms 279 1066 global 279 1066</span><br style="font-family: 'courier new', monospace; "><span style="font-family: 'courier new', monospace; "> Improper Dih. atoms 279 1066 1210 904 global 279 1066 1210 904</span><br style="font-family: 'courier new', monospace; "><br style="font-family: 'courier new', monospace; "><span style="font-family: 'courier new', monospace; ">-------------------------------------------------------</span><br style="font-family: 'courier new', monospace; "><span style="font-family: 'courier new', monospace; ">Program mdrun, VERSION 4.6.3</span><br style="font-family: 'courier new', monospace; "><span style="font-family: 'courier new', monospace; ">Source code file: /src/gromacs-4.6.3/src/mdlib/domdec_top.c, line: 393</span><br style="font-family: 'courier new', monospace; "><br style="font-family: 'courier new', monospace; "><span style="font-family: 'courier new', monospace; ">Fatal error:</span><br style="font-family: 'courier new', monospace; "><span style="font-family: 'courier new', monospace; ">3 of the 103492 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1.4 nm) or the two-body cut-off distance (1.4 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck</span><br style="font-family: 'courier new', monospace; "><span style="font-family: 'courier new', monospace; ">For more information and tips for troubleshooting, please check the GROMACS</span><br style="font-family: 'courier new', monospace; "><span style="font-family: 'courier new', monospace; ">website at </span><a href="http://www.gromacs.org/Documentation/Errors" style="font-family: 'courier new', monospace; ">http://www.gromacs.org/Documentation/Errors</a><br style="font-family: 'courier new', monospace; "><span style="font-family: 'courier new', monospace; ">-------------------------------------------------------</span><br style="font-family: 'courier new', monospace; "></div></body></html>