commands (c47b2)
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
* analys: Analysis facility
* apbs: Adaptive Poisson-Boltzmann Solver
* aspenr: Atomic Solvation Parameter Based Energy
* aspenrmb: ASP Model with Implicit Membrane
* axd: Accelerated Dynamics module
* blade: BLaDE GPU Basic Lambda Dynamics Engine 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
* corman: 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
* dimens: Set maximum dimension parameters for this charmm run.
* dims: Dynamic IMportance Sampling
* drude: Drude oscillator commands
* dynamc: 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
* genborn: Generalized Born Solvation Energy
* gbim: Generalized Born with Implicit Membrane
* gbmv: Generalized Born Using Molecular Volume
* gbsw: Generalized Born with a simple SWitching
* galgor: The genetic algorithm commands
* gnn: Genetic Neural Network
* graphx: The graphics subsection for workstations
* hbonds: Generation of hydrogen bonds
* hbuild: Construction of hydrogen positions
* hqbm: Biased Molecular Dyanmics
* images: Use of periodic or crystal environment
* intcor: Manipulation of internal coordinates
* io: 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
* miscom: 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
* nbonds: Generation of the non-bonded interaction
* overlap: Overlap of Molecular Similarity
* parmfile: CHARMM energy parameters
* pbeq: Poisson-Boltzmann Equation Solver
* pert: 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
* qmmm: 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
* struct: Structure manipulation (PSF generation)
* subst: Command line substitution parameters
* tamd: Torsion Angle Molecular Dynamics
* test: Commands to test various things
* tmd: Targeted Molecular Dynamics
* rtop: Residue Topology File
* torque: Manipulate torques
* tpcntrl: Temperature and pressure control
* tps: Transition Path Sampling
* trek: Reaction coordinate refinement command
* perturb: Thermodynamic Simulation Method
* umbrel: Umbrella Sampling
* valbond: VALBOND-trans force field
* vibran: Vibrational analysis facility
* zerom: Zero-Order Minimization
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
* analys: Analysis facility
* apbs: Adaptive Poisson-Boltzmann Solver
* aspenr: Atomic Solvation Parameter Based Energy
* aspenrmb: ASP Model with Implicit Membrane
* axd: Accelerated Dynamics module
* blade: BLaDE GPU Basic Lambda Dynamics Engine 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
* corman: 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
* dimens: Set maximum dimension parameters for this charmm run.
* dims: Dynamic IMportance Sampling
* drude: Drude oscillator commands
* dynamc: 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
* genborn: Generalized Born Solvation Energy
* gbim: Generalized Born with Implicit Membrane
* gbmv: Generalized Born Using Molecular Volume
* gbsw: Generalized Born with a simple SWitching
* galgor: The genetic algorithm commands
* gnn: Genetic Neural Network
* graphx: The graphics subsection for workstations
* hbonds: Generation of hydrogen bonds
* hbuild: Construction of hydrogen positions
* hqbm: Biased Molecular Dyanmics
* images: Use of periodic or crystal environment
* intcor: Manipulation of internal coordinates
* io: 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
* miscom: 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
* nbonds: Generation of the non-bonded interaction
* overlap: Overlap of Molecular Similarity
* parmfile: CHARMM energy parameters
* pbeq: Poisson-Boltzmann Equation Solver
* pert: 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
* qmmm: 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
* struct: Structure manipulation (PSF generation)
* subst: Command line substitution parameters
* tamd: Torsion Angle Molecular Dynamics
* test: Commands to test various things
* tmd: Targeted Molecular Dynamics
* rtop: Residue Topology File
* torque: Manipulate torques
* tpcntrl: Temperature and pressure control
* tps: Transition Path Sampling
* trek: Reaction coordinate refinement command
* perturb: Thermodynamic Simulation Method
* umbrel: Umbrella Sampling
* valbond: VALBOND-trans force field
* vibran: Vibrational analysis facility
* zerom: Zero-Order Minimization