NAMD

NAMD is a molecular dynamics program designed for parallel computation. Full and efficient treatment of electrostatic and van der Waals interactions are provided via the Particle Mesh Ewald algorithm. NAMD interoperates with CHARMM and X-PLOR as it uses the same force field and includes a rich set of MD features (multiple time stepping, constraints, and dissipative dynamics).

NAMD Molecular Dynamics Software Non-Exclusive, Non-Commercial Use License.

Availability / Target HPC systems

We are currently in the process of providing modules on Woody, TinyGPU, and Emmy. All these modules will be based on pre-built official binaries distributed by the developers of NAMD.

There will be no NAMD module on Meggie for the time being.

Notes

none yet

Sample job scripts

serial job on Woody 

#!/bin/bash -l
#PBS -lnodes=1:ppn=4,walltime=01:00:00
#PBS -N name

cd $PBS_O_WORKDIR

module load namd/2.14-multicore

namd2 +p4 input.conf > logfile

parallel job on Emmy 

#!/bin/bash -l
#PBS -lnodes=2:ppn=40,walltime=01:00:00
#PBS -N name

cd $PBS_O_WORKDIR

module load namd/2.14-verbs-smp

PPN=40

namd2 +p$PPN +idlepoll ++ppn $PPN input.conf > logfile

single GPU job on TinyGPU 

#!/bin/bash -l
#PBS -lnodes=1:ppn=4:v100:smt,walltime=01:00:00
#PBS -N name

cd $PBS_O_WORKDIR

module load namd/2.14-multicore-cuda

namd2 +p8 input.conf > logfile

Further information

Mentors