Documentation

If you are using CHARMM for the first time, you may want to start here and read the installation instructions.

Below is the documentation of the latest version of CHARMM. For additional help, please visit the Forum.

Frequently used modules

  • Coordinate manipulation and analysis / corman
  • Energy commands / energy
  • Non-bonded options / nbonds
  • Minimization / minimiz
  • Molecular dynamics / dynamc
  • Constraints and restraints / cons
  • Time series and correlation functions / correl
  • Atom selections / select

Modules in alphabetical order

abpo / ace / adumb / afm / analys / apbs / aspenr / aspenrmb / axd / block / cadpac / cca / cff / cfti / changelog / charmm / charmmrate / cheq / cmake / commands / cons / consph / corman / correl / corsol / cross / crystl / csa / developer / diesel / dimens / dims / domdec / drude / dynamc / eds / eef1 / emap / energy / ensemble / epmf / ewald / facts / fitcharge / fitparam / flucq / fmm / fourd / g09 / galgor / gamess / gamess-uk / gamus / gbim / gbmv / gbsw / genborn / gnn / gopair / gpu / graphx / grid / hbonds / hbuild / hqbm / images / install / intcor / io / larmord / lonepair / lupopt / mc / mcma / minimiz / miscom / mmff / mmff_params / mmfp / mmpt / mndo97 / molvib / monitor / mrmd / mscale / mtp / mtpl / mts / nbonds / nmr / nose / openmm / overlap / parallel / parmfile / pbeq / pdetail / pert / perturb / phmd / pimplem / pipf / pnm / preflx_list / prefx / pressure / primo / proto / qchem / qmmm / qturbo / qub / random / rdc / rdfsol / repdstr / replica / rism / rtop / rush / rxncons / sasa / sbound / scalar / sccdftb / scpism / select / sgld / shapes / shell / ssnmr / stringm / struct / subst / support / tamd / test / testcase / tmd / torque / tpcntrl / tps / trek / umbrel / usage / valbond / vibran / zerom

Complete list of modules

  • Adaptively Biased Path Optimization (ABPO) Method / abpo
  • Analytical Continuum Solvent (ACS) Potential / ace
  • Adaptive Umbrella Sampling Module / adumb
  • The AFM Module of CHARMM / afm
  • Analysis Commands / analys
  • Adaptive Poisson-Boltzmann Solver (APBS) / apbs
  • Atomic Solvation Parameter Based Energy / aspenr
  • Atomic Solvation Parameter Model with Implicit Membrane / aspenrmb
  • The AXD Module of CHARMM / axd
  • Partion molecular system into blocks / block
  • Combined Quantum Mechanical and Molecular Mechanics Method / cadpac
  • Common Component Architecture / cca
  • Consistent Force Field (CFF) / cff
  • CFTI: conformational energy/free energy calculations / cfti
  • CHARMM Developer's Change Log / changelog
  • Chemistry at HARvard Macromolecular Mechanics / charmm
  • CHARMM/POLYRATE INTERFACE / charmmrate
  • The CHarge EQuilibration Method / cheq
  • Using CMake to install CHARMM / cmake
  • CHARMM commands / commands
  • CONSTRAINTS / cons
  • Monte-carlo method for constant pH simulations / consph
  • The Coordinate Manipulation Commands / corman
  • Correlation Functions / correl
  • Solvent Correlation Functions / corsol
  • Reactive Molecular Dynamics with Surface Crossing / cross
  • Calculations on Crystals using CHARMM / crystl
  • Distributed CSA (Conformational Space Annealing) Command / csa
  • CHARMM Developer Guide / developer
  • Combined Quantum Mechanical and Molecular Mechanics Method / diesel
  • How to set CHARMM to run with any size system / dimens
  • Dynamic Importance Sampling (DIMS) / dims
  • Domain Decomposition / domdec
  • Polarizable Drude Oscillator Format / drude
  • Dynamics: Description and Discussion / dynamc
  • Enveloping Distribution Sampling Method / eds
  • Effective Energy Function 1 / eef1
  • The EMAP module / emap
  • Energy Manipulations: Minimization and Dynamics / energy
  • ENSEMBLE averaging / replica exchange / ensemble
  • EPMF Module of CHARMM / epmf
  • The Ewald Summation method / ewald
  • FACTS: Fast Analytical Continuum Treatment of Solvation / facts
  • The Charge and Drude Polarizability Fitting / fitcharge
  • Parameter Fitting Procedure / fitparam
  • Combined QM/MM Fluctuating Charge Potential for CHARMM / flucq
  • Fast Multipole Method (FMM) for Nonbond Interactions / fmm
  • 4 Dimension dynamics: Description and Discussion / fourd
  • Combined Quantum Mechanical and Molecular Mechanics Method / g09
  • Galgor: Commands which deal with Genetic Algorithm and Monte Carlo. / galgor
  • Combined Quantum Mechanical and Molecular Mechanics Method / gamess
  • Combined Quantum Mechanical and Molecular Mechanics Method / gamess-uk
  • Gaussian Mixture Adaptive Umbrella Sampling (GAMUS) / gamus
  • Generalized Born Solvation Energy Module with Implicit Membrane / gbim
  • Generalized Born using Molecular Volume (GBMV) / gbmv
  • Generalized Born with a simple SWitching (GBSW) / gbsw
  • Generalized Born Solvation Energy and Forces Module / genborn
  • Genetic Neural Network / gnn
  • The Go pairwise Energy Module of CHARMM / gopair
  • Installing and running CHARMM on GPU / gpu
  • GRAPHICS / graphx
  • Grid: A general facility to implment grid-based potentials for docking / grid
  • Generation of Hydrogen Bonds / hbonds
  • Construction of hydrogen positions / hbuild
  • The HQBM Module of CHARMM / hqbm
  • IMAGES / images
  • CHARMM Release and Installation / install
  • The Internal Coordinate Manipulation Commands / intcor
  • Input-Output Commands / io
  • LARMORD: A Distance-based Chemical Shift Predictor / larmord
  • Lone Pair Facility / lonepair
  • Low Energy Path OPTmization / lupopt
  • Monte Carlo / mc
  • Monte Carlo Minimization/Annealing (MCMA) / mcma
  • Energy Manipulations: Minimization and Dynamics / minimiz
  • Miscellaneous Commands / miscom
  • Merck Molecular Force Field (MMFF94) / mmff
  • The MMFF94 Setup Procedure And Parameter Files / mmff_params
  • Miscellaneous mean field potentials / mmfp
  • Molecular Mechanics with Proton Transfer (MMPT) / mmpt
  • Combined Quantum Mechanical and Molecular Mechanics Method / mndo97
  • The MOLVIB Module of CHARMM / molvib
  • Monitor commands: Commands to monitor various dynamics properties / monitor
  • Multi-Surface Adiabatic Reactive Molecular Dynamics (MS-ARMD) / mrmd
  • Multi Scale Command: MSCALE / mscale
  • Multipole Module / mtp
  • Spherical Multipole Electrostatic Module using Local / mtpl
  • Multiple Time Scales Method (MTS) / mts
  • Generation of Non-bonded Interactions / nbonds
  • NMR Analysis Module / nmr
  • The documentation of Nose-Hoover method - Masa Watanabe / nose
  • OpenMM GPU acceleration interface to CHARMM / openmm
  • Overlap of Molecular Similarity / overlap
  • Parallel Implementation of CHARMM / parallel
  • CHARMM Emprical Energy Function Parameters / parmfile
  • Poisson-Bolztmann Equation Module / pbeq
  • Details about TSM Free Energy Calculations / pdetail
  • Free Energy Perturbation Calculations / pert
  • Perturbation: Thermodynamic Perturbation Calculations. / perturb
  • Continuous constant pH Molecular Dynamics (PHMD) / phmd
  • Implementation of the Thermodynamic Simulation Method / pimplem
  • Polarizable Intermolecular Potential Functions (PIPF) / pipf
  • Plastic Network Model (PNM) / pnm
  • LIST OF ALL COMPILE (##) KEYWORDS IN CHARMM / preflx_list
  • CHARMM Preprocessing / prefx
  • Constant Pressure/Temperature (CPT) Dynamics / pressure
  • PRIMO Module of CHARMM / primo
  • Prototypes / proto
  • Combined Quantum Mechanical and Molecular Mechanics Method / qchem
  • Combined Quantum and Molecular Mechanical Hamiltonian / qmmm
  • A Quantum Mechanical / Molecular Mechanical (QM/MM) Interface / qturbo
  • Closed and Open Polymer Chain Path-Integral Methods for QM/MM / qub
  • Random Number Generator Controlling Commands / random
  • Residual Dipolar coupling (RDC) module / rdc
  • Radial Correlation Functions / rdfsol
  • The Parallel Distributed Replica / repdstr
  • Replica: Commands which deal with replication of the molecular system: Replica. / replica
  • RISM (Reference Interaction Site Model) module / rism
  • Residue Topology File / rtop
  • RUSH: A simple implicit-solvent force-field for protein simulation / rush
  • Rxncons: Commands for holonomic constrains of different order parameters / rxncons
  • The SASA implicit solvation model / sasa
  • Method and implementation of deformable boundary forces / sbound
  • SCALar : commands to manipulate scalar atom properties / scalar
  • Combined Quantum Mechanical and Molecular Mechanics Method / sccdftb
  • Screened Coulomb Potentials Implicit Solvent Model (SCPISM) / scpism
  • ATOM SELECTION / select
  • Self-Guided Langevin Dynamics (SGLD) / sgld
  • Shape Descriptors / shapes
  • Shell Decomposition / shell
  • Solid State NMR (SSNMR) Energy Functions / ssnmr
  • String method for the study of conformational transitions / stringm
  • Generation and Manipulation of the Structure (PSF) / struct
  • Command Line Substitution Parameters / subst
  • Support Programs and Data Files / support
  • Torsion Angle Molecular Dynamics (TAMD) Module / tamd
  • Test commands: Commands to test various conditions in CHARMM / test
  • CHARMM Testcases / testcase
  • Targeted Molecular Dynamics / tmd
  • Manipulating torques: TORQUE / torque
  • Temperature and pressure control / tpcntrl
  • Transition Path Sampling / tps
  • TReK: a program for Trajectory REfinement and Kinematics. / trek
  • Order Parameters / umbrel
  • How to use CHARMM / usage
  • VALBOND-TRANS / valbond
  • Vibration Analysis / vibran
  • The Z Module is a general facility for carrying out conformational / zerom