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
- 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