Nanoscale Molecular Dynamics (NAMD)
Overview
Nanoscale Molecular Dynamics (NAMD) is used to simulate the movement of atoms in a molecular structure over time. Capable of scaling across a large amount of nodes and CPU cores through its use of Charm++, NAMD is known for being highly performant and excels at using parallelization on computing clusters to simulate massive structures.
NAMD also supports the use of GPUs through CUDA and pairs well with VMD to show a visual representation of NAMD's results.
Availability
| Cluster | Module/Version |
|---|---|
| BOSE | namd/2.14 namd/2.14-cuda test-namd/3.0 test-namd/3.0-cuda |
| BGSC | namd/2.13 namd/2.13-cuda |
Note: You can simply use module load namd to activate the most recently installed version of this software.
Sample Slurm Script
#!/bin/bash
# -- SLURM SETTINGS -- #
# [..] other settings here [..]
# The following settings are for the overall request to Slurm
#SBATCH --ntasks-per-node=32 # How many CPU cores do you want to request
#SBATCH --nodes=1 # How many nodes do you want to request
# -- SCRIPT COMMANDS -- #
# Load the needed modules
module load namd # Load Nanoscale Molecular Dynamics (NAMD)
namd +setcpuaffinity +ppn ${SLURM_NTASKS} inputfile.namd > results.out
Real Example
Has your research group used Nanoscale Molecular Dynamics (NAMD) in a project? Contact the HPC Team and we'd be glad to feature your work.
Citation
Please include the following citation in your papers to support continued development of Nanoscale Molecular Dynamics (NAMD).
James C. Phillips, David J. Hardy, Julio D. C. Maia, John E. Stone, Joao V. Ribeiro, Rafael C. Bernardi, Ronak Buch, Giacomo Fiorin, Jerome Henin, Wei Jiang, Ryan McGreevy, Marcelo C. R. Melo, Brian K. Radak, Robert D. Skeel, Abhishek Singharoy, Yi Wang, Benoit Roux, Aleksei Aksimentiev, Zaida Luthey-Schulten, Laxmikant V. Kale, Klaus Schulten, Christophe Chipot, and Emad Tajkhorshid. Scalable molecular dynamics on CPU and GPU architectures with NAMD. Journal of Chemical Physics, 153:044130, 2020. doi:10.1063/5.0014475