Thank You for Quick reply Justin... On Sat, Jun 2, 2012 at 8:58 PM, Justin A. Lemkul <[email protected]> wrote:
> > You'll get a mismatch in your files (checkpoint, trajectory, energy) in > terms of frame interval. You should not try to append to these files or > extend the run. Just run a new simulation from 20 -> 30 ns. The grompp > command was correct, assuming you set "tinit = 20000" in the .mdp file and > setting nsteps appropriately to give another 10 ns. Then run it as a new > simulation. It will still be an extension of the first simulation (since > the .cpt preserves the previous state), but without the mdrun -cpi -append > mechanism, which in this case you don't want (or possibly can't use) I will follow your advice.. > Second query; >> >> To rerun the crash run, users give .cpt file as input to -mdrun, >> My query is, There are two cpt file a) pre.cpt b) .cpt , >> So which one has to given as input??? >> >> >> Use gmxcheck to understand the contents of each. The timestamp will >> also >> tell you a difference, as will reading mdrun -h for an explanation of >> what >> the -cpt option is doing >> >> >> As per the link..http://www.gromacs.org/**Documentation/File_Formats/** >> Checkpoint_File<http://www.gromacs.org/Documentation/File_Formats/Checkpoint_File> >> I interpreted following things.. >> >> 1. I have to use the state.cpt , but in the case problem to these I have >> to use >> prev.cpt, I can check there >> content by gmxcheck.. >> >> But my Query is What are may be the potential problems ?? and how to >> find >> them ?? >> >> Crash the run is very often with my system, that why I am worried.. >> >> > If you're getting frequent crashes, you should investigate why this is > happening rather than just plowing ahead. Are there error messages in the > .log or stdout/stderr output? Are your energetic terms sensible? If the > system is crashing due to physical instability, you're wasting your time > producing junk. If the crashes are occurring due to hardware or filesystem > instability, that's something to take up with your sysadmin. > > > -Justin > Thank you For Advice...
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