ID=262

• Dataset: 6n4o
• Software: NAMD3.cuda (namd-multicore/3.0.1-gfbfc-2023a-avx512)
• Resource: 1 tasks, 4 cores, 1 nodes, 4 GPUs, with NVLink
• CPU: EPYC 9654 (Genoa), 2.4 GHz
• GPU: NVidia-H100-SXM5-80GB, 16 cores/GPU
• Simulation speed: 109.233 ns/day
• Efficiency: 40.8 %
• Site: Rorqual
• Date: Aug. 20, 2025, 2:05 a.m.
• Submission script:

  #!/bin/bash
  #SBATCH -c4 --gpus-per-node=h100:4 --mem-per-cpu=2000 --time=20:0
  
  module --force purge
  module load StdEnv/2023 gcc/12.3 cuda/12.2 namd-multicore/3.0.1
  
  # Run simulation 
  namd3 +p${SLURM_CPUS_PER_TASK} +idlepoll namd3_input.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
  numsteps 800000
  outputtiming 100000
  
  # Output 
  restartfreq         100000      
  dcdfreq             100000 
  outputEnergies      2000
  outputPressure      100000 
  outputname          _prod
  
  # AMBER FF settings
  amber on
  rigidBonds     all 
  useSettle      on 
  rigidTolerance 1.0e-8 
  cutoff         8.0 
  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
  GPUresident 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