c42b1

commands

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