<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Hi Andrew, I have just repeated this tutorial. There is nothing wrong with that.</div><div><div><br></div><div>Download all the files again and repeat the tutorial from the beginning. </div><div>It can be a file that was corrupted during your previous download or you did something wrong in one of the steps.</div><div><br></div><div>You can copy&paste the following lines to your terminal. Sit down and relax. </div><div>If that doesn't work you have a problem with your gromacs installation.</div><div><br></div><div><br></div><div>#start copy</div><div><br></div><div>wget <a href="http://lindahl.sbc.su.se/outgoing/workshop2007/tutorial1/1LYD.pdb">http://lindahl.sbc.su.se/outgoing/workshop2007/tutorial1/1LYD.pdb</a></div><div><div><div>wget <a href="http://lindahl.sbc.su.se/outgoing/workshop2007/tutorial1/em.mdp">http://lindahl.sbc.su.se/outgoing/workshop2007/tutorial1/em.mdp</a></div></div><div>wget <a href="http://lindahl.sbc.su.se/outgoing/workshop2007/tutorial1/pr.mdp">http://lindahl.sbc.su.se/outgoing/workshop2007/tutorial1/pr.mdp</a></div><div>wget <a href="http://lindahl.sbc.su.se/outgoing/workshop2007/tutorial1/run.mdp">http://lindahl.sbc.su.se/outgoing/workshop2007/tutorial1/run.mdp</a></div><div><br></div><div>#run the whole thing </div><div>echo 5 | pdb2gmx -f 1LYD.pdb -water tip3p</div><div>editconf -f conf.gro –bt dodecahedron –d 0.5 –o box.gro</div><div>genbox_d -cs -cp box.gro -p topol.top -o solvated.gro </div><div>grompp -v -f em.mdp -c solvated.gro -p topol.top -o em</div><div>mdrun -v -deffnm em </div><div>grompp -v -f pr.mdp -c em.gro -t em.trr -p topol.top -o pr </div><div>mdrun -v -deffnm pr </div></div><div>grompp -v -f run.mdp -c pr.gro -t pr.trr -p topol.top -o md</div><div>mdrun -v -deffnm md</div><div><br></div><div>#end copy</div><div><br></div><div><br></div><div><br></div><div><div>Diego.</div><div><br></div><div>--</div><div>=========================================</div><div>Diego Enry B Gomes | PhD Student @ UFRJ - Brazil</div><div>/tmp/home/@ Pacific Northwest National Laboratory</div><div><div>Richland, WA. +1 (509) 372.6363 </div><div><a href="mailto:diegoenry.gomes@pnl.gov">diegoenry.gomes@pnl.gov</a></div><div>=========================================</div></div><div><div><br></div><div>On Mar 10, 2009, at 12:36 AM, Andrew Voronkov wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Dear GROMACS users,<br>I'm doing this tutorial:<br><a href="https://extras.csc.fi/chem/courses/gmx2007/tutorial1/tutorial1.pdf">https://extras.csc.fi/chem/courses/gmx2007/tutorial1/tutorial1.pdf</a> <br>and I have an error with dt=0.002 or even dt=0.001 in pr.mdp during equilibration. It works only with dt=0.0001 which seems very very small step for me. Is it ok or I need to clean up the warnings like in error below(it's for dt=0.002):<br><br>starting mdrun 'T4-*LYPOZYME in water'<br>25000 steps, 50.0 ps.<br>Warning: 1-4 interaction between 2 and 20 at distance 2.619 which is larger than the 1-4 table size 2.000 nm<br>These are ignored for the rest of the simulation<br>This usually means your system is exploding,<br>if not, you should increase table-extension in your mdp file<br>or with user tables increase the table size<br><br>t = 0.000 ps: Water molecule starting at atom 100062 can not be settled.<br>Check for bad contacts and/or reduce the timestep.<br><br>Back Off! I just backed up step0b.pdb to ./#step0b.pdb.1#<br><br>Back Off! I just backed up step0c.pdb to ./#step0c.pdb.1#<br>Wrote pdb files with previous and current coordinates<br>step 0Segmentation fault<br>andrew@linux-f29d:~/GROMACS_MD/1LYD> <br><br>Here is pr.mdp:<br><br>integrator = md<br>nsteps = 25000<br>dt = 0.001<br>nstlist = 10<br>rlist = 1.0<br>coulombtype = pme<br>rcoulomb = 1.0<br>vdw-type = cut-off<br>rvdw = 1.0<br>tcoupl = Berendsen<br>tc-grps = protein non-protein<br>tau-t = 0.1 0.1<br>ref-t = 298 298<br>Pcoupl = Berendsen<br>tau-p = 1.0<br>compressibility = 5e-5 5e-5 5e-5 0 0 0<br>ref-p = 1.0<br>nstenergy = 100<br>define = -DPOSRES<br><br><br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at http://www.gromacs.org/search before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br></div></blockquote></div><br></div></div></body></html>