Running and Verification

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Go to the Amber21 test case directory.

   cd /path/to/AMBER/amber21/AmberTools/benchmarks/nab

3. Modify the bench_amber file.
   1. Open the bench_amber file.

      vi bench_amber

   2. Press i to enter the edit mode and modify the file as follows:

      #!/bin/sh
          sander=sander.MPI
          cat<<EOF > mdin
                 benchmark a short md
          &cntrl
                 igb=1, cut=20.0, rgbmax=20.0,
                 tempi=50.0, temp0=100.0, tautp=0.4, ntt=1,
                 ntb=0, nstlim=1000, ntpr=10,
                 ntx=1, irest=0,
                 ntc=2, ntf=2, tol=0.0000001,
          /
      EOF
      $DO_PARALLEL $sander -O -i mdin -p $1.top -c $1.mc.x -o $1.md.o
      /bin/rm mdin restrt mdinfo

   3. Press Esc, type :wq!, and press Enter to save the file and exit.
4. Perform the computing.

   nab bench_md.nab
   time ./bench_md gcn4dna

   The following is an example of the output result.