NAMD Guide

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You need following modules:

module load namd/2.10-ibverbs mpi/openmpi/1.6.5-gcc

The script for submission will be:

#!/bin/tcsh -f
#SBATCH -J fhvtest2           # job name
#SBATCH -o fhvtest.o%j       # output and error file name (%j expands to jobID)
#SBATCH -n 36               # total number of mpi tasks requested
#SBATCH --ntasks-per-node=36 # cores per node
#SBATCH -p generalsky          # queue (partition)

charmrun +p$SLURM_NTASKS ++mpiexec ++remote-shell \
         "srun --mpi=pmi2 --resv-port" /apps/namd/2.10-ibverbs/namd2 \
         $workdir/namd_pentamer_equil.conf > quil.out # use srun command instead of mpirun.