Thank you very much for your quick replies,
Seems there is no wall clock set: d47fvj@milano:~/VOTCA-play_around$ grep mdrun inverse.log run_gromacs.sh: No walltime defined, so time limitation given to mdrun Running critical command 'mdrun -s topol.tpr -c confout.gro -o traj.trr -x traj.xtc' :-) mdrun (-: starting mdrun 'cg-c12' And if I look into the inverse.log the last thing is: d47fvj@milano:~/VOTCA-play_around$ tail inverse.log NODE (s) Real (s) (%) Time: 44.510 70.053 63.5 (Mnbf/s) (MFlops) (ns/day) (hour/ns) Performance: 3.327 502.271 7.772 3.088 gcq#356: "Never, I said never, compare with experiment" (Magnus Bergh) Simulation is not finished, but a checkpoint was found, so it seems walltime is nearly up, stopping now, resume csg_inverse whenever you want. d47fvj@milano:~/VOTCA-play_around$ I have also tried running mmdrun before submitting for the iterations and it was running. (Going to try in the step 001 now) On Aug 18, 4:07 pm, Christoph Junghans <jungh...@votca.org> wrote: > Hi Valentina, > > have a look at inverse.log to see if and how mdrun was executed: > $grep mdrun inverse.log > > if no walltime is given, the output should look like: > run_gromacs.sh: No walltime defined, so time limitation given to mdrun > Running critical command 'mdrun -s topol.tpr -c confout.gro -o > traj.trr -x traj.xtc' > :-) mdrun (-: > starting mdrun 'CG water' > > You can also go in step_001 and run mdrun by hand to see what happens. > > Cheers, > > Christoph > > 2011/8/18 Valentina <valentina_erast...@yahoo.co.uk>: > > > > > Hello, sorry for so many questions. > > > I am currently trying to run csg_inverse. I am not setting any > > walltime and I am getting the following: > > > Doing iteration 1 (dir step_001) > > Incomplete step 1 > > Simulation with gromacs > > Simulation is not finished, but a checkpoint was found, so it seems > > walltime is nearly up, stopping now, resume csg_inverse whenever you > > want. > > > Seems I cannot get further then step 1, even if I restart the > > calculation or do it with a set wall time for a large number. It is > > only a tryal run, so there are nto many steps to be done, so the > > calculation itself is taking very little time. > > > Thank you very much for your help, > > V > > > -- > > You received this message because you are subscribed to the Google Groups > > "votca" group. > > To post to this group, send email to votca@googlegroups.com. > > To unsubscribe from this group, send email to > > votca+unsubscr...@googlegroups.com. > > For more options, visit this group > > athttp://groups.google.com/group/votca?hl=en. > > -- > Dr. Christoph Junghans > Votca Core Developer > > Web:http://www.votca.org -- You received this message because you are subscribed to the Google Groups "votca" group. To post to this group, send email to votca@googlegroups.com. To unsubscribe from this group, send email to votca+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/votca?hl=en.