CHARMM

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

Download CHARMM:

wget https://www.charmm.org/charmm/download/current/charmm.tar.gz
tar xzf charmm.tar.gz

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

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