run_md_simulations.sh

#!/bin/bash

###########################################################
# run_md_simulations.sh
# Author: Senal Liyanage
# Affiliation: Mississippi State University
# Contact: sliyanage@tougaloo.edu
# Date: June 4, 2023
# Description: Bash script for running MD simulations
###########################################################

# Usage message
usage() {
    echo
    echo "USAGE: run_md_simulations.sh [SYSTEM NAME] [CPU] [0/1] [GPU INDEX] [MD Start] [MD Stop] [TRAJECTORY NUMBER]"
    echo
    echo "For preproduction run, set the third argument to 0."
    echo "For production run, set the third argument to 1."
    echo
    exit
}

# Check the number of arguments
if [ $# -lt 3 ]; then
    usage
else
    echo "$(date): Running MD Simulations..."
fi

# Set variables based on the arguments
system_name=$1
cpu_cores=$2
simulation_type=$3
gpu_index=$4
md_start=$5
md_stop=$6
trajectory_number=$7

# Log variable values
echo "System name: $system_name"
echo "Number of CPU cores: $cpu_cores"
echo "Simulation type: $simulation_type"

# Function for preproduction run
preproduction_run() {
    # Minimize the system's energy with constraints decreasing over time.
    echo "$(date): Starting minimization stage..."
    mpirun -np $cpu_cores pmemd.MPI -O -p $system_name.parm7 -c $system_name.rst7 -i 001.min/minimize.in -o 001.min/min.log -inf 001.min/$system_name-min.info -x 001.min/$system_name-min.nc -r 001.min/$system_name-min.rst -ref $system_name.rst7
    if [ $? -eq 0 ]; then
        echo "$(date): Minimization completed successfully."
    else
        echo "$(date): Minimization failed. Check the log file for details."
        exit 1
    fi

    # Heat the system to 310K with constraints.
    echo "$(date): Starting first heating stage..."
    mpirun -np $cpu_cores pmemd.MPI -O -p $system_name.parm7 -c 001.min/$system_name-min.rst -i 002.heat/heat-with-constraints.in -o 002.heat/$system_name-heat.log -inf 002.heat/$system_name-heat.info -x 002.heat/$system_name-heat.nc -r 002.heat/$system_name-heat.rst -ref $system_name.rst7
    if [ $? -eq 0 ]; then
        echo "$(date): First heating completed successfully."
    else
        echo "$(date): First heating failed. Check the log file for details."
        exit 1
    fi

    echo "$(date): Starting second heating stage..."
    mpirun -np $cpu_cores pmemd.MPI -O -p $system_name.parm7 -c 002.heat/$system_name-heat.rst -i 002.heat/heat-with-constraints2.in -o 002.heat/$system_name-heat2.log -inf 002.heat/$system_name-heat2.info -x 002.heat/$system_name-heat2.nc -r 002.heat/$system_name-heat2.rst -ref $system_name.rst7
    if [ $? -eq 0 ]; then
        echo "$(date): Second heating completed successfully."
    else
        echo "$(date): Second heating failed. Check the log file for details."
        exit 1
    fi
}

# Function for production run
production_run() {
    # Check if necessary arguments are available
    if [ -z "$gpu_index" ] || [ -z "$md_start" ] || [ -z "$md_stop" ] || [ -z "$trajectory_number" ]; then
        echo "$(date): Missing arguments for production run."
        exit
    fi

    # Select a CUDA device and run NPT MD simulations until the target simulation length is reached (nmax+1).
    export CUDA_VISIBLE_DEVICES=$gpu_index

    cd Traj${trajectory_number}/003.equil || { echo "$(date): Could not change to directory Traj${trajectory_number}/003.equil"; exit 1; }

    echo "$(date): Starting equilibration stage..."
    # Equilibrate the system with constraints.
    mpirun -np $cpu_cores pmemd.MPI -O -p ../../$system_name.parm7 -c ../../002.heat/$system_name-heat2.rst -i equil.1.in -o $system_name-equil.1.log -inf $system_name-equil.1.info -x $system_name-equil.1.nc -r $system_name-equil.1.rst -ref ../../$system_name.rst7
    mpirun -np $cpu_cores pmemd.MPI -O -p ../../$system_name.parm7 -c $system_name-equil.1.rst -i equil.2.in -o $system_name-equil.2.log -inf $system_name-equil.2.info -x $system_name-equil.2.nc -r $system_name-equil.2.rst -ref ../../$system_name.rst7
    mpirun -np $cpu_cores pmemd.MPI -O -p ../../$system_name.parm7 -c $system_name-equil.2.rst -i equil.3.in -o $system_name-equil.3.log -inf $system_name-equil.3.info -x $system_name-equil.3.nc -r $system_name-equil.3.rst -ref ../../$system_name.rst7
    mpirun -np $cpu_cores pmemd.MPI -O -p ../../$system_name.parm7 -c $system_name-equil.3.rst -i equil.4.in -o $system_name-equil.4.log -inf $system_name-equil.4.info -x $system_name-equil.4.nc -r $system_name-equil.4.rst

    cd ../004.prod
    echo "$(date): Starting production stage..."

    # Production
    if [ $md_start == "0" ]; then
        $AMBERHOME/bin/pmemd.cuda -O -p ../../$system_name.parm7 -c ../003.equil/$system_name-equil.4.rst -i production.in -o $system_name-md0.log -inf $system_name-md0.info -x $system_name-md0.nc -r $system_name-md0.rst
        nrun=1
    else
        nrun=$md_start
    fi

    prev=$(expr $nrun - 1)
    nmax=$md_stop

    while [ $nrun -le $nmax ]; do
        $AMBERHOME/bin/pmemd.cuda -O -p ../../$system_name.parm7 -c $system_name-md$prev.rst -i production.in -o $system_name-md$nrun.log -inf $system_name-md$nrun.info -x $system_name-md$nrun.nc -r $system_name-md$nrun.rst
        prev=$nrun
        nrun=$(expr $nrun + 1)
    done
}

# Main script execution
if [ $simulation_type == "0" ]; then
    preproduction_run
elif [ $simulation_type == "1" ]; then
    production_run
else
    echo "Invalid argument for simulation type. Exiting simulation."
    usage
fi