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 inter-operates 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#
NAMD comes with a license which prohibits us to "just install and everyone can use it". We, therefore, need individual users to print and sign the NAMD license. Subsequently, we will set the permissions accordingly.
On Alex and TinyGPU, we provide the official pre-built
Linux-x86_64-multicore-CUDA (NVIDIA CUDA acceleration) binary; use module avail namd to find the binaries.
Sample job scripts#
single GPU job on TinyGPU#
#!/bin/bash -l
#SBATCH --gres=gpu:1
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=8
#SBATCH --time=10:00:00
#SBATCH --job-name=my-namd
unset SLURM_EXPORT_ENV
module load namd/2.14-multicore-cuda
cd $SLURM_SUBMIT_DIR
namd2 +p 8 +setcpuaffinity my-project.conf > my-project.out