CHARMM commands
The commands available for use in CHARMM are classified in
several groups.
* Menu:
* Analysis: (analys.doc ). Analysis facility
* ACE: (ace.doc ). Analytical Continuum Electrostatics
* ADUMB: (adumb.doc ). ADaptive UMBrella sampling simulation
* Block: (block.doc ). BLOCK free energy simulation
* Cons: (cons.doc ). Harmonic and other constraints or SHAKE
* Coordinates: (corman.doc ). Commands to manipulate coordinates
* Correl: (correl.doc ). Time series and correlation functions
* Crystl: (crystl.doc ). Crystal facility
* Dynamics: (dynamc.doc ). Dynamics commands
* EEF1: (eef1.doc ). Effective Energy Function 1
* Energy: (energy.doc ). Energy evaluation
* Ewald: (ewald.doc ). Ewald summation
* GBorn: (genborn.doc ). Generalized Born Solvation Energy
* 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
* 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
* Minimiz: (minimiz.doc ). Description of the minimization methods
* Miscellany: (miscom.doc ). Miscellaneous commands
* MMFP: (mmfp.doc ). Miscelaneous Mean Field Potential
* Molvib: (molvib.doc ). Molecular vibrational analysis facility
* NMR: (nmr.doc ). NMR analysis facility
* Non-bonded: (nbonds.doc ). Generation of the non-bonded interaction
* Parameters: (parmfile.doc). CHARMM energy parameters
* PBEQ: (pbeq.doc ). Poisson-Boltzmann Equation Solver
* Perturb: (pert.doc ). Free energy perturbation simulations
* Pressure: (pressure.doc). Pressure calculation and usage
* Quantum: (qmmm.doc ). Quantum and Molecular Mechanical FF
* Replica: (replica.doc ). REPLICA: molecular system replication
* RISM: (rism.doc ). Reference Interaction Site Model
* Sbound: (sbound.doc ). Stoichastic boundary
* Scalar: (scalar.doc ). Scalar command for atom properties
* Select: (select.doc ). Use of the atom selection facility
* Structure: (struct.doc ). Structure manipulation (PSF generation)
* Substitute: (subst.doc ). Command line substitution parameters
* Test: (test.doc ). Commands to test various things
* Topology: (rtop.doc ). Residue Topology File
* Travel: (travel.doc ). Reaction coordinate refinement command
* TSM: (perturb.doc ). Thermodynamic Simulation Method
* Umbrella: (umbrel.doc ). Umbrella Sampling
* Vibration: (vibran.doc ). Vibrational analysis facility
* MMFF: (mmff.doc ). Merck Molecular Force Field
CHARMM Documentation / Rick_Venable@nih.gov