Overview

NAMD2 is the 1992 release of the NAMD program introducing new features

- Reads CHARMM (or X-PLOR) formatted parameter files.
- Supports periodic and non-periodic MD simulations.
- Particle mesh Ewald full electrostatics for periodic simulations.
- Triple timestepping.
- Rigid bonds to hydrogen atoms.
- Fixed atoms implemented efficiently, no unnecessary force calculations.
- Berendsen and Langevin piston constant pressure methods.
- Steered Molecular Dynamics (SMD) features.

How to use

We provide the following builds of NAMD2:

  • namd2 - multinode, MPI needed
  • namd2-node - single node, no GPU support
  • namd2-gpu - multinode with GPU support, MPI needed
  • namd2-node-gpu - single node with GPU support
  • namd2-plumed  - multinode, plumed support, MPI needed

Suffix -gpu is GPU version; -node is for OMP version (can run on 1 node only) 

An example PBS script to run NAMD2 with mpirun i.e. namd2, namd2-gpu, namd2-plumed binaries will look like:

#!/bin/bash

#PBS -l walltime=20:00:00
#PBS -l mem=256GB
#PBS -l ncpus=96
#PBS -l software=namd
#PBS -l wd

# Load module, always specify version number.
module load namd/2.14


# For namd2 MPI builds you will need to module load openmpi
module load openmpi/4.0.2

# Must include `#PBS -l storage=scratch/ab12+gdata/yz98` if the job
# needs access to `/scratch/ab12/` and `/g/data/yz98/`

mpirun -np $PBS_NCPUS namd2 input.namd > output


To run multicopy NAMD2 e.g. for replica exchange needs the namd2 or namd2-gpu binaries and the script will look like:

#!/bin/bash

#PBS -l walltime=20:00:00
#PBS -l mem=256GB
#PBS -l ncpus=96
#PBS -l software=namd
#PBS -l wd

# Load module, always specify version number.
module load namd/2.14


# For namd2 MPI builds you will need to module load openmpi
module load openmpi/4.0.2

# Must include `#PBS -l storage=scratch/ab12+gdata/yz98` if the job
# needs access to `/scratch/ab12/` and `/g/data/yz98/`

# create separate folders for the output of M=8 replicas
mkdir -p output
(cd output; mkdir -p {0..7})

# run a simulation with M=8 replicas
mpirun -np $PBS_NCPUS namd2 +replicas 8 apoa1.namd +stdout output/%d/apoa1.%d.log
The multicopy builds for NAMD2 are not optimum and it is highly advised to move to NAMD3.


NAMD2 on GPUs has been optimised for the single node build for which a sample PBS script will look like

#!/bin/bash

#PBS -q gpuvolta
#PBS -l walltime=20:00:00
#PBS -l mem=192GB
#PBS -l ngpus=4
#PBS -l ncpus=48
#PBS -l software=namd
#PBS -l wd

# Load module, always specify version number.
module load namd/2.14

# Must include `#PBS -l storage=scratch/ab12+gdata/yz98` if the job
# needs access to `/scratch/ab12/` and `/g/data/yz98/`

namd2-node-gpu +p $PBS_NCPUS +setcpuaffinity +devices 0,1,2,3 input.namd > output