NAMD#
NAMD is a molecular dynamics application designed for large biomolecular systems (proteins, nucleic acids, lipid bilayers). On Aire, NAMD 2.14 is available via the module system and runs under MPI.
Available versions on Aire#
Version |
Load Command |
|---|---|
2.14 |
|
NAMD documentation: NAMD website
Licensing#
NAMD is distributed under a non-commercial license by the University of Illinois (TCBG). For license terms, see NAMD license
How to submit a job#
Download the ApoA1 benchmark#
cd ~
wget https://www.ks.uiuc.edu/Research/namd/utilities/apoa1.tar.gz
tar -zxvf apoa1.tar.gz
Submit a CPU MPI job#
#!/bin/bash
#SBATCH --job-name=namd2_mpi
#SBATCH --output=%x_%j.log
#SBATCH --error=%x_%j.log
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=4
#SBATCH --time=01:00:00
module purge
module load namd/2.14/gcc-14.2.0_openmpi-5.0.6
# Note: To reduce CPU usage while waiting on messages, you can enable Charm++ idle polling:
# Add '+idelpoll' to the NAMD command. This may improve system responsiveness on shared nodes,
# but can slightly reduce performance on tightly coupled parallel jobs.
# Example:
# mpirun -np 4 namd2 +idelpoll ~/apoa1/apoa1.namd
mpirun -np 4 namd2 ~/apoa1/apoa1.namd
Generate structure files with psfgen#
#!/bin/bash
#SBATCH --job-name=namd2_psfgen
#SBATCH --output=%x_%j.log
#SBATCH --time=00:05:00
module purge
module load namd/2.14/gcc-14.2.0_openmpi-5.0.6
cd ~/apoa1
psfgen << EOF
resetpsf
readpsf apoa1.psf
coordpdb apoa1.pdb
writepsf apoa1_test.psf
writepdb apoa1_test.pdb
EOF
Notes#
Replace file names to match your input files. Adjust ntasks and time limits based on your workload.