ID=55

• Dataset: 6n4o
• Software: NAMD3.cuda (binary_pack/3.0a9------)
• Resource: 1 tasks, 2 cores, nodes, 2 GPUs, no NVLink
• CPU: Xeon E5-2650 (Sandy Bridge), 2.2 GHz
• GPU: Tesla-P100-PCIE-12GB, 16 cores/GPU
• Simulation speed: 9.93187 ns/day
• Efficiency: 56.5 %
• Site: Cedar
• Date: Nov. 30, 2021, 6:40 p.m.
• Submission script:

• Notes:

  #SBATCH -c2 --gpus=p100:2 --nodes=1

• Simulation input file:

  # Amber/(t,s,x)leap generated parm and crd file  
  parmfile       prmtop.parm7
  ambercoor      inpcrd.rst7
  # GPU-resident integrator
  CUDASOAintegrate on
  numsteps 10000
  # Input 
  bincoordinates  equilibration.coor
  binvelocities   equilibration.vel
  extendedsystem  equilibration.xsc
  # Output 
  restartfreq         10000
  dcdfreq             10000
  outputEnergies      10000
  outputPressure      10000
  outputname          equilibration
  # AMBER FF 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
  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