Related Software

GROMOS

A molecular dynamics simulation package for biomolecular systems.

Overview

GROMOS is a molecular dynamics simulation package that provides a comprehensive set of tools for studying biomolecular systems. It is particularly well-suited for studying proteins, nucleic acids, and lipids.

Features

  • Molecular dynamics simulations
  • Energy minimization
  • Free energy calculations
  • Structure prediction
  • Custom force field development
  • Enhanced sampling methods

Installation

Requirements

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

Installation Steps

  1. Download GROMOS: 
    wget https://www.gromos.net/downloads/gromos.tar.gz
tar xzf gromos.tar.gz
  2. Configure and build: 
    cd gromos
mkdir build
cd build
cmake ..
make -j 4

Basic Usage

Example Script

# Energy minimization
minimize protein.pdb

# Molecular dynamics
dynamics protein.pdb 1000 1.0 2.0 2.0

# Free energy calculation
free_energy protein.pdb

Advanced Topics

Force Fields

GROMOS supports various force fields:

  • GROMOS96
  • GROMOS05
  • GROMOS11

Performance Optimization

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