<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><div>Dear Gromacs Users,</div><div><br></div><div>I am trying to run g_cluster to find an average structure for my system and after giving the following command line:</div><div><br></div><div>g_cluster_d -f allnj10_XM10.xtc -s EB_XM.gro -cl pdb_ligplot<span style="font-style: italic">_</span>XM.pdb -n –g</div><div><br></div><div>g_cluster started without problems and continued calculating the matrix etc…until I got this:</div><div><br></div><div><div>Last frame 5000 time 50000.004 </div><div>Allocated 645448320 bytes for frames</div><div>Read 5001 frames from trajectory allnj10_XM10.xtc</div><div>Computing 5001x5001 RMS deviation matrix</div><div># RMSD calculations left: 0 </div><div><br></div><div>The RMSD ranges from 0.0816802 to 0.301369 nm</div><div>Average RMSD is 0.208468</div><div>Number of structures for matrix 5001</div><div>Energy of the matrix is 364.532 nm</div><div>WARNING: rmsd minimum 0 is below lowest rmsd value 0.0816802</div><div>Linking structures **************</div><div>Sorting and renumbering clusters</div><div><br></div><div>Found 1425 clusters</div><div><br></div><div>Writing middle structure for each cluster to pdb_ligplot_XM.pdb</div><div>Segmentation fault: 11</div></div><div><br></div><div>Can you please help me to understand where the problem comes from and how I can solve it? </div><div>Any help is greatly appreciated. </div><div><br></div><div>Thank you.</div><div>Davide</div></body></html>