CHARMM commands
The commands available for use in CHARMM are classified in
several groups.
ABPO / Adaptively Biased Path Optimization
ACE / Analytical Continuum Electrostatics
ADUMB / ADaptive UMBrella sampling simulation
AFM / Atomic Force Microscopy Simulation
Analysis / Analysis facility
APBS / Adaptive Poisson-Boltzmann Solver
ASPENER / Atomic Solvation Parameter Based Energy
ASPENERMB / ASP Model with Implicit Membrane
AXD / Accelerated Dynamics module
Block / BLOCK free energy simulation
CCA / Common Component Architecture
CFF / Consistent Force Field (CFF)
CHEQ / CHarge EQuilibration Methods
Cons / Harmonic and other constraints or SHAKE
CHARMMrate / CHARMM-POLYRATE Interface
Coordinates / Commands to manipulate coordinates
Correl / Time series and correlation functions
Corsol / Solvent Correlation Functions
Cross / Reactive MD with Surface Crossing
Crystl / Crystal facility
CSA / Conformational Space Annealing
Dimension / Set maximum dimension parameters for this charmm run.
DIMS / Dynamic IMportance Sampling
Drude / Drude oscillator commands
Dynamics / Dynamics commands
DIESEL / QM/MM method interface to DIESEL(GAMESS)
Domdec / Domain Decomposition Code
EEF1 / Effective Energy Function 1
EMAP / The MAP Object Manipulation Commands
Energy / Energy evaluation
Ensemble / Run communicating copies of CHARMM
EPMF / Distance and angle based energy terms
Ewald / Ewald summation
FACTS / Fast Analytical Continuum Solvation Model
FitCharge / Charge and Drude Polarizability Fitting
FitParam / Parameter Fitting Procedure
FlucQ / QM/MM Fluctuating Charge Potential
FMM / Fast Multipole Method for Nonbond Interactions
G09 / QM/MM Based on Gaussian09
Gamus / Gaussian Mixture Adaptive Umbrella Sampling
GBorn / Generalized Born Solvation Energy
GBIM / Generalized Born with Implicit Membrane
GBMV / Generalized Born Using Molecular Volume
GBSW / Generalized Born with a simple SWitching
Genetic / The genetic algorithm commands
GNN / Genetic Neural Network
Graphx / The graphics subsection for workstations
H-bond / Generation of hydrogen bonds
H-build / Construction of hydrogen positions
HQBM / Biased Molecular Dyanmics
Images / Use of periodic or crystal environment
Internal / Manipulation of internal coordinates
I/O / I/O of data structures and files
LonePair / Lone-Pair Facility
LUPOPT / Low Energy Path OPTimization
MC / Monte Carlo simulation program
MCMA / Monte Carlo Minimization / Annealing
Minimiz / Description of the minimization methods
Miscellany / Miscellaneous commands
MMFF / Merck Molecular Force Field
MMFP / Miscelaneous Mean Field Potential
MMPT / Molecular Mechanics with Proton Transfer
MNDO97 / QM/MM method based on MNDO97
Molvib / Molecular vibrational analysis facility
MRMD / Multi-Surface Adiabatic Reactive MD
MS-EVB / Multi-State Empirical Valence Bond
Mscale / Multi Scale Command: MSCALE
MTP / Distributed Multipole facility
NMR / NMR analysis facility
Non-bonded / Generation of the non-bonded interaction
Overlap / Overlap of Molecular Similarity
Parameters / CHARMM energy parameters
PBEQ / Poisson-Boltzmann Equation Solver
Perturb / Free energy perturbation simulations
PHMD / Continuous constant pH Molecular Dynamics
PIPF / Polarizable Intermolecular Pot Functions
PNM / Plastic network mode commands
Pressure / Pressure calculation and usage
PRIMO / PRIMO potential terms
PROTO / Prototype commands
QCHEM / QMMM method using Q-CHEM interface
Qturbo / QMMM method using TURBOMOL interface
Quantum / Quantum and Molecular Mechanical FF
Qub / Quantized Classical Path Sampling
RDC / Residual Dipolar coupling (RDC) module
RDFSol / Radial correlation functions
Repdstr / The Parallel Distributed Replica
Replica / REPLICA: molecular system replication
RISM / Reference Interaction Site Model
RUSH / A simple implicit solvent force field
RXNCONS / Reaction coordinate constraints
SASA / The SASA implicit solvation model
Sbound / Stoichastic boundary
Scalar / Scalar command for atom properties
SCCDFTB / QM/MM method interface to SCCDFTB
SCPISM / SCP Implicit Solvent Model
Select / Use of the atom selection facility
Shell / Shell decomposition
SGLD / Self-Guided Langevin Dynamics
SSNMR / Solid State NMR (SSNMR) Energy Functions
Stringm / 0-K String Method
Structure / Structure manipulation (PSF generation)
Substitute / Command line substitution parameters
TAMD / Torsion Angle Molecular Dynamics
Test / Commands to test various things
TMD / Targeted Molecular Dynamics
Topology / Residue Topology File
TORQue / Manipulate torques
TPCONTROL / Temperature and pressure control
TPS / Transition Path Sampling
Travel / Reaction coordinate refinement command
TSM / Thermodynamic Simulation Method
Umbrella / Umbrella Sampling
Valbond / VALBOND-trans force field
Vibration / Vibrational analysis facility
Zerom / Zero-Order Minimization