CHARMM c39b2 commands.doc
CHARMM commands
The commands available for use in CHARMM are classified in
several groups.
* Menu:
* ABPO: (abpo.doc ). Adaptively Biased Path Optimization
* ACE: (ace.doc ). Analytical Continuum Electrostatics
* ADUMB: (adumb.doc ). ADaptive UMBrella sampling simulation
* AFM: (afm.doc ). Atomic Force Microscopy Simulation
* Analysis: (analys.doc ). Analysis facility
* APBS: (apbs.doc ). Adaptive Poisson-Boltzmann Solver
* ASPENER: (aspenr.doc ). Atomic Solvation Parameter Based Energy
* ASPENERMB: (aspenrmb.doc). ASP Model with Implicit Membrane
* AXD: (axd.doc ). Accelerated Dynamics module
* Block: (block.doc ). BLOCK free energy simulation
* CCA: (cca.doc ). Common Component Architecture
* CFF: (cff.doc ). Consistent Force Field (CFF)
* CHEQ: (cheq.doc ). CHarge EQuilibration Methods
* Cons: (cons.doc ). Harmonic and other constraints or SHAKE
* CHARMMrate: (charmmrate.doc). CHARMM-POLYRATE Interface
* Coordinates: (corman.doc ). Commands to manipulate coordinates
* Correl: (correl.doc ). Time series and correlation functions
* Corsol: (corsol.doc ). Solvent Correlation Functions
* Cross: (cross.doc ). Reactive MD with Surface Crossing
* Crystl: (crystl.doc ). Crystal facility
* CSA: (csa.doc ). Conformational Space Annealing
* Dimension: (dimens.doc ). Set maximum dimension parameters for this charmm run.
* DIMS: (dims.doc ). Dynamic IMportance Sampling
* Drude: (drude.doc ). Drude oscillator commands
* Dynamics: (dynamc.doc ). Dynamics commands
* DIESEL: (diesel.doc ). QM/MM method interface to DIESEL(GAMESS)
* Domdec: (domdec.doc ). Domain Decomposition Code
* EEF1: (eef1.doc ). Effective Energy Function 1
* EMAP: (emap.doc ). The MAP Object Manipulation Commands
* Energy: (energy.doc ). Energy evaluation
* Ensemble: (ensemble.doc). Run communicating copies of CHARMM
* EPMF: (epmf.doc ). Distance and angle based energy terms
* Ewald: (ewald.doc ). Ewald summation
* FACTS: (facts.doc ). Fast Analytical Continuum Solvation Model
* FitCharge: (fitcharge.doc). Charge and Drude Polarizability Fitting
* FitParam: (fitparam.doc). Parameter Fitting Procedure
* FlucQ: (flucq.doc ). QM/MM Fluctuating Charge Potential
* G09: (g09.doc ). QM/MM Based on Gaussian09
* Gamus: (gamus.doc ). Gaussian Mixture Adaptive Umbrella Sampling
* GBorn: (genborn.doc ). Generalized Born Solvation Energy
* GBIM: (gbim.doc ). Generalized Born with Implicit Membrane
* GBMV: (gbmv.doc ). Generalized Born Using Molecular Volume
* GBSW: (gbsw.doc ). Generalized Born with a simple SWitching
* Genetic: (galgor.doc ). The genetic algorithm commands
* GNN: (gnn.doc ). Genetic Neural Network
* Graphx: (graphx.doc ). The graphics subsection for workstations
* H-bond: (hbonds.doc ). Generation of hydrogen bonds
* H-build: (hbuild.doc ). Construction of hydrogen positions
* HQBM: (hqbm.doc ). Biased Molecular Dyanmics
* Images: (images.doc ). Use of periodic or crystal environment
* Internal: (intcor.doc ). Manipulation of internal coordinates
* I/O : (io.doc ). I/O of data structures and files
* LonePair : (lonepair.doc). Lone-Pair Facility
* LUPOPT : (lupopt.doc ). Low Energy Path OPTimization
* MC: (mc.doc ). Monte Carlo simulation program
* MCMA: (mcma.doc ). Monte Carlo Minimization / Annealing
* Minimiz: (minimiz.doc ). Description of the minimization methods
* Miscellany: (miscom.doc ). Miscellaneous commands
* MMFF: (mmff.doc ). Merck Molecular Force Field
* MMFP: (mmfp.doc ). Miscelaneous Mean Field Potential
* MMPT: (mmpt.doc ). Molecular Mechanics with Proton Transfer
* MNDO97 (mndo97.doc ). QM/MM method based on MNDO97
* Molvib: (molvib.doc ). Molecular vibrational analysis facility
* MRMD: (mrmd.doc ). Multi-Surface Adiabatic Reactive MD
* Mscale: (mscale.doc ). Multi Scale Command: MSCALE
* MTP: (mtp.doc ). Distributed Multipole facility
* NMR: (nmr.doc ). NMR analysis facility
* Non-bonded: (nbonds.doc ). Generation of the non-bonded interaction
* Overlap: (overlap.doc ). Overlap of Molecular Similarity
* Parameters: (parmfile.doc). CHARMM energy parameters
* PBEQ: (pbeq.doc ). Poisson-Boltzmann Equation Solver
* Perturb: (pert.doc ). Free energy perturbation simulations
* PHMD: (phmd.doc ). Continuous constant pH Molecular Dynamics
* PIPF: (pipf.doc ). Polarizable Intermolecular Pot Functions
* PNM: (pnm.doc ). Plastic network mode commands
* Pressure: (pressure.doc). Pressure calculation and usage
* PRIMO: (primo.doc ). PRIMO potential terms
* PROTO: (proto.doc ). Prototype commands
* QCHEM: (qchem.doc ). QMMM method using Q-CHEM interface
* Qturbo: (qturbo.doc ). QMMM method using TURBOMOL interface
* Quantum: (qmmm.doc ). Quantum and Molecular Mechanical FF
* Qub: (qub.doc ). Quantized Classical Path Sampling
* RDFSol: (rdfsol.doc ). Radial correlation functions
* Repdstr: (repdstr.doc ). The Parallel Distributed Replica
* Replica: (replica.doc ). REPLICA: molecular system replication
* RISM: (rism.doc ). Reference Interaction Site Model
* RUSH: (rush.doc ). A simple implicit solvent force field
* RXNCONS: (rxncons.doc ). Reaction coordinate constraints
* SASA: (sasa.doc ). The SASA implicit solvation model
* Sbound: (sbound.doc ). Stoichastic boundary
* Scalar: (scalar.doc ). Scalar command for atom properties
* SCCDFTB: (sccdftb.doc ). QM/MM method interface to SCCDFTB
* SCPISM: (scpism.doc ). SCP Implicit Solvent Model
* Select: (select.doc ). Use of the atom selection facility
* Shell: (shell.doc ). Shell decomposition
* SGLD: (sgld.doc ). Self-Guided Langevin Dynamics
* Stringm: (stringm.doc ). 0-K String Method
* Structure: (struct.doc ). Structure manipulation (PSF generation)
* Substitute: (subst.doc ). Command line substitution parameters
* TAMD: (tamd.doc ). Torsion Angle Molecular Dynamics
* Test: (test.doc ). Commands to test various things
* TMD: (tmd.doc ). Targeted Molecular Dynamics
* Topology: (rtop.doc ). Residue Topology File
* TORQue: (torque.doc ). Manipulate torques
* TPCONTROL: (tpcntrl.doc ). Temperature and pressure control
* TPS: (tps.doc ). Transition Path Sampling
* Travel: (trek.doc ). Reaction coordinate refinement command
* TSM: (perturb.doc ). Thermodynamic Simulation Method
* Umbrella: (umbrel.doc ). Umbrella Sampling
* Valbond: (valbond.doc ). VALBOND-trans force field
* Vibration: (vibran.doc ). Vibrational analysis facility
* Zerom: (zerom.doc ). Zero-Order Minimization