Thank you for reply. The calculation runs, I have grompp.gro and a traj.trr, but I indeed don't have entry for the nstxtcout in my grompp and hence no traj.xtc. Will go fix it ASAP.
V On Aug 18, 8:23 pm, Christoph Junghans <[email protected]> wrote: > Is there a confout.gro in step_001? > Do you specify the right trajectory type in cg.inverse.gromacs.traj_type. > The default is xtc, but if you set nstxtcout in grompp.mdp to 0, the > xtc file is not created. > > Cheers, > > Christoph > > 2011/8/18 Valentina <[email protected]>: > > > > > > > > > > > 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 <[email protected]> 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 <[email protected]>: > > >> > 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 [email protected]. > >> > To unsubscribe from this group, send email to > >> > [email protected]. > >> > 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 [email protected]. > > To unsubscribe from this group, send email to > > [email protected]. > > 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 [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/votca?hl=en.
