TINKER Tutorial

Introduction

This tutorial will guide you through the installation, configuration, and basic usage of TINKER. TINKER is a powerful molecular mechanics and dynamics simulation package that supports various force fields and algorithms.

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 TINKER

                            wget https://dasher.wustl.edu/tinker/downloads/tinker-8.10.1.tar.gz

                            tar -xzf tinker-8.10.1.tar.gz

                            cd tinker-8.10.1

                            

                            # Compile

                            cd source

                            make -f Makefile.gfortran

                            

                            # Set environment variables

                            echo 'export TINKER_HOME=/path/to/tinker-8.10.1' >> ~/.bashrc

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

                            source ~/.bashrc

Note: Make sure to replace the TINKER_HOME path with your actual installation path.

Basic Usage

1. Prepare Input File

Create a TINKER input file (example.xyz):


                            3

                            H2O Example

                            O1    0.0000    0.0000    0.0000    1    2    3

                            H2    0.9572    0.0000    0.0000    1    2    3

                            H3   -0.2400    0.9270    0.0000    1    2    3

2. Run Energy Minimization


                            # Energy minimization using AMBER force field

                            minimize example.xyz 1000 0.0001

                            

                            # Energy minimization using CHARMM force field

                            minimize example.xyz 1000 0.0001 -k charmm

3. Run Molecular Dynamics Simulation


                            # Run NVT ensemble simulation

                            dynamic example.xyz 1000 1.0 2.0 2.0 298.0

                            

                            # Run NPT ensemble simulation

                            dynamic example.xyz 1000 1.0 2.0 2.0 298.0 -p 1.0

Advanced Topics

1. Free Energy Calculations

TINKER 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 dynamic example.xyz 1000 1.0 2.0 2.0 298.0

Introduction
Installation Steps
Basic Usage
Advanced Topics