Running and Verifying AmberTools

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Run the following command to go to the case directory of AmberTools 18:

   cd /path/to/AMBER/amber18/AmberTools/benchmarks/nab

3. Run the following commands to modify the bench_amber file:
   1. Open bench_amber.

      vi bench_amber

   2. Press i to enter the insert mode and modify the bench_amber file.

      #!/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 changes and exit.
4. Run the following command to perform parallel computing:

   ./bench_amber halfam0

   View the ns/day value in the halfam0.md.o log file. A larger value indicates better performance.

   Figure 1 shows an example of the output result.

   Figure 1 An example result