ID=163

• Dataset: 4cg1
• Software: SANDER.QUICK.cuda.MPI (ambertools/21-gofbc-2020.1.403.114-avx2)
• Resource: 16 tasks, 1 cores, nodes, 16 GPUs, with NVLink
• CPU: Xeon Silver 4216 (Cascade Lake), 2.1 GHz
• GPU: Tesla-V100-SXM2-32GB, 8 cores/GPU
• Simulation speed: 0.0116741 ns/day
• Efficiency: 32.5 %
• Site: Cedar
• Date: Feb. 9, 2022, 11:12 p.m.
• Submission script:

  #!/bin/bash
  #SBATCH -A def-svassili
  #SBATCH --ntasks=16 --cpus-per-task=1 --nodes=4
  #SBATCH --gpus-per-task=v100l:1 
  #SBATCH --mem-per-cpu=4000 --time=02:00:00
  
  module load StdEnv/2020 gcc/9.3.0 cuda/11.0 openmpi/4.0.3 ambertools/21 
  source $EBROOTAMBERTOOLS/amber.sh 
  
  srun sander.quick.cuda.MPI -O -i B3LYP.in -p complex_solv_PNP.prmtop -c mini-QMMM_4.rst -ref mini-QMMM_4.rst -o stdout

• Notes:

• Simulation input file:

  Applying constraints on specific distances of the substrate specially Ser-substrate, substrate-W185, Meth
  &cntrl
    nstlim=40, dt=0.001, 
    ntpr=2, ntwr=1000, ntwx=1000,
    ntt=3, temp0=310.0, gamma_ln=1.0, ig=-1,
    taup=2.0,
    ntc=2, ntf=2, iwrap=1,
    cut = 12.0,
    ntr=0, 
    nmropt=0,
   ifqnt=1
  /
  &qmmm
  iqmatoms=840,841,842,843,844,845,846,847,848,1914,1915,1916,1917,1918,1919,1920,1921,1922,1905,1906,1907,1908,1909,1910,1911,1912,1913,3943,3944,3946,3948,3947,3942,3945,3949,3950,3951,3952,3953,3954,3955,3956,3957,3958,3959,3960,3961,
    qmcharge=0,
    spin=1
    qm_theory="quick",
    qmmm_int=5, 
    qm_ewald=0,
  /
  &quick
    method = "B3LYP",
    basis = "6-31G*",
  /