ID=199

• Dataset: 4cg1
• Software: SANDER.QUICK.cuda.MPI (ambertools/21-gofbc-2020.1.403.114-avx2)
• Resource: 12 tasks, 1 cores, nodes, 12 GPUs, with NVLink
• CPU: EPYC 7413 (Milan), 2.65 GHz
• GPU: NVIDIA-A100-SXM4-40GB, 12 cores/GPU
• Simulation speed: 0.0144048 ns/day
• Efficiency: 30.1 %
• Site: Narval
• Date: Aug. 4, 2023, 8:18 p.m.
• Submission script:

  #!/bin/bash
  #SBATCH -A def-svassili
  #SBATCH --ntasks=12 --cpus-per-task=1
  #SBATCH --gpus-per-task=1 
  #SBATCH --mem-per-cpu=4000 --time=02:00:00
  
  module purge
  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

• Notes:

  QM/MM, B3LYP/6-31G*

  0.0127697
  0.0140146
  0.0141965
  0.0143379
  0.0144048

• 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*",
  /