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NAMD

NAMD (NAnoscale Molecular Dynamics) is a parallel molecular dynamics code designed for fast simulation of large biomolecular systems on large-scale parallel computers. NAMD uses empirical force fields, such as Amber, CHARMM, and Dreiding, to compute atomic trajectories by numerically solving the equations of motion. NAMD supports simulations with over 200,000 cores.

1. Script Template​

submit.sh
#!/bin/bash
#SBATCH --nodes=1                   # Number of nodes
#SBATCH --ntasks-per-node=56        # Number of cores per node
#SBATCH --ntasks=56                 # Total number of cores
#SBATCH --partition=g1_share        # Queue partition; must specify the correct partition
#SBATCH --job-name=hello            # Job name
#SBATCH --output=hello.%j.out       # Normal log output (%j parameter value is jobId)
#SBATCH --error=hello.%j.err        # Error log output (%j parameter value is jobId)
   
##############################################
#          Software Envrironment             #
##############################################
unset I_MPI_PMI_LIBRARY                        # Unset default MPI library, use Intel's built-in
export I_MPI_JOB_RESPECT_PROCESS_PLACEMENT=0   # Parameter modification required for Intel multi-node jobs
module load intel/2022 intelmpi/2022           # Load Intel environment
   
##############################################
#               Run job                      #
##############################################
export OMP_NUM_THREADS=1
   
namd2 +ppn 56 $input_file