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  1. #!/bin/bash
  2. # job name
  3. #$ -N amber_5uj1
  4. # use current environment and run in the current working directory
  5. #$ -V -cwd
  6. # run for 48hrs and only run on whole nodes
  7. #$ -l h_rt=48:00:00
  8. #$ -l coproc_k80=1
  9. # load the modules
  10.  
  11. module load amber/16gpu
  12. module load cuda
  13.  
  14. # run program
  15. pmemd.cuda -O -i /nobackup/cmcmf/amber/01_Min_C.in -o /nobackup/cmcmf/amber/5uj1_min.out -p /nobackup/cmcmf/amber/5uj1.prmtop -c /nobackup/cmcmf/amber/5uj1.inpcrd -r /nobackup/cmcmf/amber/5uj1_min.restrt -ref /nobackup/cmcmf/5uj1.inpcrd
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