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 TinyGPU and Alex. 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

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

Further information

Mentors