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commands (c43b2)

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
» 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