NAMD2

##============================================================
# NAMD Production MD Configuration Template - duhpc Cluster
# For CHARMM force field simulations
# Usage: reference this file in namd_gpu.sh
#============================================================

# ── Input files ───────────────────────────────────────────
structure          system.psf         ;# CHARMM PSF topology
coordinates        system.pdb         ;# Initial coordinates

# ── Force field parameters ────────────────────────────────
paraTypeCharmm     on
parameters         par_all36_prot.prm
parameters         par_all36_lipid.prm
parameters         toppar_water_ions.str
# Add more parameter files as needed

# ── Output files ──────────────────────────────────────────
outputName         production
restartfreq        5000               ;# Save restart every 10 ps
dcdfreq            5000               ;# Save trajectory every 10 ps
outputEnergies     500                ;# Print energies every 1 ps
outputPressure     500

# ── Restart (comment out for new simulation) ──────────────
# bincoordinates     equil.restart.coor
# binvelocities      equil.restart.vel
# extendedSystem     equil.restart.xsc

# ── Initial temperature (comment out if using restart) ────
temperature        300

# ── Basic MD settings ─────────────────────────────────────
exclude            scaled1-4
1-4scaling         1.0
cutoff             12.0
switching          on
switchdist         10.0
pairlistdist       14.0

# ── Integrator ────────────────────────────────────────────
timestep           2.0                ;# 2 fs timestep
rigidBonds         all                ;# SHAKE on all H bonds
nonbondedFreq      1
fullElectFrequency 2

# ── Electrostatics (PME) ──────────────────────────────────
PME                yes
PMEGridSpacing     1.0

# ── Periodic boundary conditions ─────────────────────────
# Set these to match your equilibrated box dimensions
cellBasisVector1   80.0  0    0
cellBasisVector2   0     80.0 0
cellBasisVector3   0     0    80.0
cellOrigin         0     0    0
wrapAll            on

# ── Temperature control (Langevin) ────────────────────────
langevin           on
langevinDamping    1.0
langevinTemp       300
langevinHydrogen   no

# ── Pressure control (Langevin piston) ───────────────────
LangevinPiston        on
LangevinPistonTarget  1.01325         ;# 1 atm in bar
LangevinPistonPeriod  100
LangevinPistonDecay   50
LangevinPistonTemp    300

# ── Run ───────────────────────────────────────────────────
# 50000000 steps x 2 fs = 100 ns
run 50000000

#!/bin/bash
#============================================================
# NAMD2 GPU Job Template - duhpc Cluster
# For CHARMM force field simulations
# NAMD2 version: 2.14 with CUDA 10 support
# Expected performance: ~39 ns/day on V100
# Usage: sbatch namd_gpu.sh
#============================================================

#SBATCH --job-name=namd_gpu         # Job name (change this)
#SBATCH --partition=gpu             # GPU partition - DO NOT CHANGE
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --gres=gpu:1                # Request 1 GPU - DO NOT CHANGE
#SBATCH --mem=16G
#SBATCH --time=2-00:00:00           # Max time (days-hours:min:sec)
#SBATCH --output=%x_%j.out
#SBATCH --error=%x_%j.err
#SBATCH --mail-type=BEGIN,END,FAIL
#SBATCH --mail-user=your@email.com  # Change to your email

#------------------------------------------------------------
# USER SETTINGS - Edit these for your simulation
#------------------------------------------------------------
CONF_FILE="namd2.conf"        # NAMD configuration file
#------------------------------------------------------------

echo "============================================="
echo "NAMD2 GPU Job - duhpc Cluster"
echo "Job ID   : $SLURM_JOBID"
echo "User     : $USER"
echo "Node     : $SLURMD_NODENAME"
echo "CPUs     : $SLURM_CPUS_PER_TASK"
echo "Start    : $(date)"
echo "============================================="

# ── NAMD2 path ────────────────────────────────────────────
NAMD2=/scratch/apps/NAMD/namd2/namd2

echo "NAMD2    : $($NAMD2 --version 2>&1 | grep 'NAMD' | grep -v Info | head -1)"
echo "GPU      : $(nvidia-smi --query-gpu=name,memory.total --format=csv,noheader)"
echo ""

# ── Check input file ──────────────────────────────────────
if [ ! -f "$CONF_FILE" ]; then
    echo "ERROR: NAMD config file not found: $CONF_FILE"
    exit 1
fi
echo "Config   : $CONF_FILE (OK)"
echo ""

# ── Run NAMD2 GPU ─────────────────────────────────────────
echo "--- Starting NAMD2 GPU MD ---"
START=$(date +%s)

$NAMD2 +p$SLURM_CPUS_PER_TASK +devices 0 $CONF_FILE

EXIT=$?
END=$(date +%s)

# ── Performance Report ────────────────────────────────────
echo ""
echo "============================================="
echo "PERFORMANCE REPORT"
echo "============================================="
if [ $EXIT -eq 0 ]; then
    echo "Status   : SUCCESS"
    echo "GPU      : $(nvidia-smi --query-gpu=name --format=csv,noheader)"
    echo "Wall time: $((END-START)) seconds"
    echo ""
    echo "Performance (ns/day):"
    grep "Benchmark time" ${CONF_FILE%.conf}.log 2>/dev/null | tail -3
    # Also check SLURM output
    grep "Benchmark time" ${SLURM_JOB_NAME}_${SLURM_JOBID}.out 2>/dev/null | tail -3
else
    echo "Status   : FAILED (exit code $EXIT)"
    echo "Check output file for details"
fi
echo "End time : $(date)"
echo "============================================="