We have mdrun integrated into our distributed computing project. When your users suspend or close the manger it checkpoints, so when they open again it continues mdrun where it left off. However, when users reboot, it starts from the beginning. We are using this command line to execute the work.
mdrun.exe (-v -x -c -o md.pdb -e -cpo md.next -cpi md.cpt -deffnm md) I have a seperate checkpoint for output so after this simulation we can extend the workunit. Should we try using this append option? Checkpoints containing the complete state of the system are written at regular intervals (option -cpt) to the file -cpo, unless option -cpt is set to -1. A simulation can be continued by reading the full state from file with option -cpi. This option is intelligent in the way that if no checkpoint file is found, Gromacs just assumes a normal run and starts from the first step of the tpr file. With checkpointing you can also use the option -append to just continue writing to the previous output files. This is not enabled by default since it is potentially dangerous if you move files, but if you just leave all your files in place and restart mdrun with exactly the same command (with options -cpi and -append) the result will be the same as from a single run. The contents will be binary identical (unless you use dynamic load balancing), but for technical reasons there might be some extra energy frames when using checkpointing (necessary for restarts without appending). -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php