Related Software

CHARMM

A versatile molecular dynamics simulation package for biomolecular systems.

Overview

CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a highly versatile and widely used molecular dynamics simulation package. It is particularly well-suited for studying biomolecular systems and includes a comprehensive set of tools for molecular modeling and simulation.

Features

  • Comprehensive force field support
  • Advanced sampling methods
  • Free energy calculations
  • QM/MM capabilities
  • Extensive analysis tools
  • Custom force field development
  • Parallel computing support

Installation

Requirements

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

Installation Steps

  1. Download CHARMM:
    wget https://www.charmm.org/charmm/download/current/charmm.tar.gz
    tar xzf charmm.tar.gz
  2. Configure and build:
    cd charmm
    mkdir build
    cd build
    cmake ..
    make -j 4

Basic Usage

Example Script

! Read topology and parameter files
read rtf card name top_all36_prot.rtf
read para card name par_all36_prot.prm

! Read protein structure
read psf card name protein.psf
read coor card name protein.pdb

! Setup periodic boundary conditions
crystal define cubic 60.0 60.0 60.0 90.0 90.0 90.0
crystal build cutoff 14.0

! Energy minimization
mini sd nstep 1000

! Molecular dynamics
dynamics verlet nstep 10000 timestep 0.002 - 
    ntrfrq 1000 nprint 100 iprfrq 1000 - 
    iunwri 20 iuncrd 30 iunvel -1 kunit 50

Advanced Topics

Free Energy Calculations

CHARMM supports various free energy calculation methods:

  • Thermodynamic Integration
  • Free Energy Perturbation
  • Umbrella Sampling
  • Metadynamics

Performance Optimization

  • Parallel computing with MPI
  • GPU acceleration (through OpenMM)
  • Memory optimization
  • Custom force field development