What to do if your work dies...

Your work has unexpectedly died. Don't worry, it happens most of the times. There will always be someone that presses the wrong button or pull a plug he was not supposed to or there will be a power cut.

So… before you go after someone, here is what to do in order to restart your work:

• Cd in /work/md/your_filename. Here there should be the heat and equi directories you had made. Create a new restart directory.

• Copy at restart the following files:

• from equi you need:
  • the ionized.psf
  • the heat_out.coor
  • the force field parameter file
  • the NAMD.sh
  • the equi.namd

• from equi/output you need:
  • the restart.coor
  • the restart.vel
  • the restart.xsc

• Now you need to make some changes at the NAMD script and the submission script .

• rename the equi.namd to restart.namd.
• edit the restart.namd and do the following:
  • at the input files add an option below coordinates named as bincoordinates with the value restart.coor.
  • at the input files change the option velocities to binvelocities and the value heat_out.vel to restart.vel.
  • at the input files at the option extendedSystem change the value heat_out.xsc to restart.xsc.
  • at the output files at the option restartname change the value output/restart to output/restart2.
  • at the end of the script set the correct values to the firsttimestep and run. In order to calculate them, edit the LOG file from equi and see what was the last step that coordinates and velocities have been written.

• edit the NAMD.sh and do the following:
  • change the name of your job from jobname_equi to jobname_res1.
  • at the last row change the equi.namd > LOG to restart.namd > LOG.

• Create an output subdirectory in restart.

• Now you are ready to submit your job by typing qsub NAMD.sh.