Related Software

TINKER

A comprehensive molecular modeling package for molecular mechanics and dynamics simulations.

Overview

TINKER is a complete and general-purpose molecular modeling package that includes molecular mechanics and dynamics capabilities. It is particularly well-suited for studying biomolecular systems and includes a comprehensive set of tools for molecular modeling and simulation.

Features

  • Molecular mechanics calculations
  • Molecular dynamics simulations
  • Energy minimization
  • Normal mode analysis
  • Free energy calculations
  • Structure prediction
  • Custom force field development

Installation

Requirements

  • Fortran compiler (GNU, Intel, or PGI)
  • MPI library (for parallel execution)
  • CMake 3.10+
  • Python 3.7+ (optional)

Installation Steps

  1. Download TINKER: 
    wget https://dasher.wustl.edu/tinker/downloads/tinker.tar.gz
tar xzf tinker.tar.gz
  2. Configure and build: 
    cd tinker
mkdir build
cd build
cmake ..
make -j 4

Basic Usage

Example Script

# Energy minimization
minimize protein.xyz

# Molecular dynamics
dynamic protein.xyz 1000 1.0 2.0 2.0

# Normal mode analysis
vibrate protein.xyz

Advanced Topics

Force Fields

TINKER supports various force fields:

  • AMBER
  • CHARMM
  • MM3
  • OPLS

Performance Optimization

  • Parallel computing with MPI
  • Memory optimization
  • Custom force field development
  • Algorithm optimization