ID=164

• Dataset: 6n4o
• Software: NAMD2.ucx (namd-ucx/2.14-iimkl-2020a-avx2)
• Resource: 8 tasks, 1 cores, nodes, 0 GPUs, no NVLink
• CPU: Xeon Platinum 8160 (Skylake), 2.1 GHz
• GPU: None
• Simulation speed: 0.38 ns/day
• Efficiency: 59.4 %
• Site: Cedar
• Date: April 28, 2022, 5:50 p.m.
• Submission script:

  #!/bin/bash
  #SBATCH -c1 --ntasks=8
  #SBATCH --mem-per-cpu=4000 --time=3:0:0
  module --force purge
  module load StdEnv/2020 intel/2020.1.217 namd-ucx/2.14
  srun --mpi=pmi2 namd2 mdin.in

• Notes:

• Simulation input file:

  # Amber/(t,s,x)leap generated parm and crd file  
  parmfile       prmtop.parm7  
  ambercoor      inpcrd.rst7
  # Input 
  bincoordinates  equilibration.coor
  binvelocities   equilibration.vel
  extendedsystem  equilibration.xsc
  # Output 
  restartfreq         10000      
  dcdfreq             10000 
  outputEnergies      10000
  outputPressure      10000 
  outputname          equilibration
  # Number of steps
  # numsteps 10000
  # AMBER Force Field settings
  amber on
  rigidBonds     all 
  useSettle      on 
  rigidTolerance 1.0e-8 
  cutoff         9.0 
  pairlistdist   11.0 
  switching      off 
  exclude        scaled1-4 
  readexclusions yes 
  1-4scaling     0.83333333 
  scnb           2.0 
  zeromomentum   on
  ljcorrection   on
  # Integrator Parameters 
  timestep            1.0 
  nonbondedFreq       1 
  fullElectFrequency  1 
  stepspercycle       10 
  wrapAll on
  # Temperature control
  langevin on
  langevinTemp 300
  langevinDamping 1.0
  # Pressure control
  useGroupPressure yes
  LangevinPiston on
  LangevinPistonTarget 1.0
  LangevinPistonPeriod 200
  LangevinPistonDecay 100
  LangevinPistonTemp 300
  # PME settings 
  PME                 on 
  PMEGridSizeX        144 
  PMEGridSizeY        144 
  PMEGridSizeZ        144