CHARMM Documentation

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
• BLaDE is a Basic Lambda Dynamics Engine for fast alchemical | blade
• Partition 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
• Distributed Charge Model (DCM) | dcm
• Distance Correlation (DCOR) | dcor
• DENBIAS Module of CHARMM | denbias
• 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
• External Bond Module | extbond
• FACTS: Fast Analytical Continuum Treatment of Solvation | facts
• FFTDOCK: An Accelerated Routine for Rigid-Protein Rigid-Ligand Docking | fftdock
• 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
• A general purpose calculator for various free energy differences using Bennett's acceptance ratio, Non-Boltzmann Bennett, and the Zwanzig equation | fren
• Full Kernel Module | fullkern
• 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
• Machine Learning Potential (MLpot) | mlpot
• 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
• Molecular Dynamics with Mobile Protons (MOBHY) | mobhy
• 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-State Empirical Valence Bond | ms-evb
• Multi Scale Command: MSCALE | mscale
• Multi-state Molecular Mechanics with Proton Transfer (MS-MMPT) | msmmpt
• 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
• Combined Quantum Mechanical and Molecular Mechanics Method | nwchem
• OpenMM GPU acceleration interface to CHARMM | openmm
• OpenMM_DOCK: An Accelerated Routine for Protein-Ligand Docking | openmm_dock
• 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
• The pycharmm Python interface to CHARMM | pycharmm
• 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
• Triatomic Kernel Module | triakern
• 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