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 at > http://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.
