Added a software application page for the NAMD software in book/softw…

book/_toc.yml

@@ -56,6 +56,7 @@ chapters:
   #   - file: software/applications/gromacs
     - file: software/applications/gaussian
     - file: software/applications/matlab
+    - file: software/applications/namd
     - file: software/applications/openfoam
     - file: software/applications/orca
     - file: software/applications/rosetta

book/software/applications/namd.md

@@ -0,0 +1,78 @@
+# 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
+<!-- List the available versions of this module on Aire -->
+<!-- Instructions on how to load this module -->
+<!-- If there are additional modules required, please mention them. -->
+
+| Version      | Load Command                                     |
+|--------------|--------------------------------------------------|
+| 2.14         | `module load namd/2.14/gcc-14.2.0_openmpi-5.0.6` |
+
+
+NAMD documentation: [NAMD website](https://www.ks.uiuc.edu/Research/namd/)
+
+## Licensing
+NAMD is distributed under a non-commercial license by the University of Illinois (TCBG). For license terms, see [NAMD license](https://www.ks.uiuc.edu/Research/namd/)
+
+## How to submit a job
+
+### Download the ApoA1 benchmark
+
+```bash
+cd ~
+wget https://www.ks.uiuc.edu/Research/namd/utilities/apoa1.tar.gz
+tar -zxvf apoa1.tar.gz
+```
+
+### Submit a CPU MPI job
+```bash
+#!/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
+
+```bash
+#!/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. 
+
+