DL_POLY Tutorial

Introduction

This tutorial will guide you through the installation, configuration, and basic usage of DL_POLY. DL_POLY is a powerful molecular dynamics simulation package that provides comprehensive tools for simulating materials science and chemistry problems.

Installation Steps

1. System Requirements

Linux/Unix system
Fortran compiler (GCC 7.0+)
4GB RAM (16GB+ recommended)
1GB disk space (10GB+ recommended)

2. Download and Compilation


                            # Download DL_POLY

                            wget https://www.ccp5.ac.uk/DL_POLY/DL_POLY_5.0.tar.gz

                            tar -xzf DL_POLY_5.0.tar.gz

                            cd DL_POLY_5.0

                            

                            # Configure and compile

                            ./configure --prefix=/path/to/install

                            make -j4

                            make install

                            

                            # Set environment variables

                            echo 'export DL_POLY_HOME=/path/to/install' >> ~/.bashrc

                            echo 'export PATH=$PATH:$DL_POLY_HOME/bin' >> ~/.bashrc

                            source ~/.bashrc

Note: Make sure to replace the installation path with your actual path. Also, ensure you have the necessary permissions to install in the chosen directory.

Basic Usage

1. Prepare Input Files

Create a DL_POLY input file (CONTROL):


                            # DL_POLY CONTROL file

                            title

                            Water simulation

                            

                            # Simulation parameters

                            timestep 0.001

                            steps 10000

                            

                            # Ensemble type

                            ensemble nvt

                            temperature 300.0

                            

                            # Output frequency

                            print 100

                            trajectory 100

2. Run Energy Minimization


                            # Energy minimization

                            dlpoly -i CONTROL -o OUTPUT -c CONFIG -f FIELD

3. Run Molecular Dynamics Simulation


                            # Run NVT ensemble simulation

                            dlpoly -i CONTROL -o OUTPUT -c CONFIG -f FIELD

                            

                            # Run NPT ensemble simulation

                            dlpoly -i CONTROL -o OUTPUT -c CONFIG -f FIELD -p 1.0

Advanced Topics

1. Free Energy Calculations

DL_POLY supports various free energy calculation methods:

Thermodynamic integration
Free energy perturbation
Umbrella sampling
Metadynamics

2. Parallel Computing

Using MPI for parallel computing:


                            # Run molecular dynamics simulation using 4 processes

                            mpirun -np 4 dlpoly -i CONTROL -o OUTPUT -c CONFIG -f FIELD

Introduction
Installation Steps
Basic Usage
Advanced Topics