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NAMD

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.

NAMD website

Installed version​

$ module avail namd

namd-2.14/openmpi-4.1.5/gcc-13.1.0

Build options:

  • interface=tcl
  • fft=3
  • backend=mpi (OpenMPI)
  • build-target=charm++

Slurm script​

Please modify this script as required:

namd.slurm
#!/bin/bash -l
## Job Script script to be adapted as required ##

#SBATCH --job-name="MY_JOB_NAME" ## <---(modify me) 
#SBATCH --output=%x.%J.out       ## %x=job name, %J=job id
#SBATCH --error=%x.%J.out
#SBATCH --time 24:00:00          ## 24h walltime ((hh:mm::ss)  <--- (modify me)
#SBATCH --partition=mpi1         ## mpi1 partition <---(modify me)
#SBATCH --ntasks=48              ## request 48 MPI tasks <---(modify me)
#SBATCH --mem=0                  ## request all node memory
#SBATCH --mail-user=<yourmail>@.yourdomain.fr   ##  <---(modify me)
#SBATCH --mail-type=END,FAIL     ## notify when job end/fail 
 
## We strongly recommend using this command
module purge

module load namd-2.14/openmpi-4.1.5
 
NAMD_SCRIPT=grap10

srun namd2 $NAMD_SCRIPT.namd > $NAMD_SCRIPT.out

Submit job to Slurm:

$ sbatch namd.slurm