CHARMM c33b2 commands.doc

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                             CHARMM commands

        The commands available for use in CHARMM are classified in
several groups.

* Menu:

* AFM:         (afm.doc     ). Atomic Force Microscopy Simulation
* Analysis:    (analys.doc  ). Analysis facility
* ACE:         (ace.doc     ). Analytical Continuum Electrostatics
* ADUMB:       (adumb.doc   ). ADaptive UMBrella sampling simulation
* APBS:        (apbs.doc    ). Adaptive Poisson-Boltzmann Solver
* ASPENER:     (chmdoc/aspener.doc ). Atomic Solvation Parameter Based Energy
* ASPENERMB:   (chmdoc/aspenermb.doc). ASP Model with Implicit Membrane
* 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 
* Crystl:      (crystl.doc  ). Crystal facility
* Drude:       (drude.doc   ). Drude oscillator commands
* Dynamics:    (dynamc.doc  ). Dynamics commands
* DIESEL:      (diesel.doc  ). QM/MM method interface to DIESEL(GAMESS)
* 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
* Ewald:       (ewald.doc   ). Ewald summation
* FitCharge:   (fitcharge.doc). Charge and Drude Polarizability Fitting
* FlucQ:       (flucq.doc   ). QM/MM Fluctuating Charge Potential
* 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
* 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
* MBOND:       (mbond.doc   ). Multi-body dynamics
* 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
* MNDO97       (mndo97.doc  ). QM/MM method based on MNDO97
* Molvib:      (molvib.doc  ). Molecular vibrational analysis 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
* Pressure:    (pressure.doc). Pressure calculation and usage
* QCHEM:       (qchem.doc   ). QMMM method using Q-CHEM interface
* Quantum:     (qmmm.doc    ). Quantum and Molecular Mechanical FF
* 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
* 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
* Structure:   (struct.doc  ). Structure manipulation (PSF generation)
* Substitute:  (subst.doc   ). Command line substitution parameters
* Test:        (test.doc    ). Commands to test various things
* TMD:         (tmd.doc     ). Targeted Molecular Dynamics
* Topology:    (rtop.doc    ). Residue Topology File
* 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
* Vibration:   (vibran.doc  ). Vibrational analysis facility