Hi Mark, Thanks for your feedback. The simulations are running now again. I got one questions, I think it will be also of interest for the others on the mailinglist. I used "grompp" with the "-t state0.cpt" option, are the starting velocities taken from the cpt files or are the assigned randomly from a Boltzman distribution. Meaning are the new simulations starting fresh or are they acontinuation from the previous ones?
Thanks, Henri On Tue, Mar 8, 2011 at 1:54 PM, Mark Abraham <mark.abra...@anu.edu.au> wrote: > On 8/03/2011 9:41 PM, Henri Mone wrote: >Ah yes, I remember now. mdrun tries to be smart and >check that all the files match the state they were in before >the crash by computing checksums when writing and again >when reading. >So the original problem was that the steps recorded in the different >.cpt are different, unsurprisingly. >To fix this, get the .mdp used to make the original .tpr, and call >grompp the same way, plus (e.g.) -t state0.cpt for each of the >replicas. Now the (matching) state information will be taken by >grompp from the (matching) checkpoint files, and no checksum >calculation can fail. Then >mdrun_mpi -multi 32 -replex 5000 -s new.tpr >should be fine (and no .cpt should be provided). >While doing this, I would avoid trying to use mdrun -append, >by the way. Glue things together later if you need to. > >Mark -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
