CHARMM Element doc/commands.doc 1.1#File: Commands, Node: Top, Up: (chmdoc/charmm.doc), Previous: (chmdoc/parallel.doc), Next: (chmdoc/install.doc) CHARMM commands The commands available for use in CHARMM are classified inseveral groups.* Menu:* Analysis: (chmdoc/analys.doc ). Analysis facility* ACE: (chmdoc/ace.doc ). Analytical Continuum Electrostatics* ADUMB: (chmdoc/adumb.doc ). ADaptive UMBrella sampling simulation* Block: (chmdoc/block.doc ). BLOCK free energy simulation* Cons: (chmdoc/cons.doc ). Harmonic and other constraints or SHAKE* CHARMMrate: (chmdoc/charmmrate.doc). CHARMM-POLYRATE Interface* Coordinates: (chmdoc/corman.doc ). Commands to manipulate coordinates* Correl: (chmdoc/correl.doc ). Time series and correlation functions * Crystl: (chmdoc/crystl.doc ). Crystal facility* Dynamics: (chmdoc/dynamc.doc ). Dynamics commands* EEF1: (chmdoc/eef1.doc ). Effective Energy Function 1* Energy: (chmdoc/energy.doc ). Energy evaluation* Ewald: (chmdoc/ewald.doc ). Ewald summation* FlucQ: (chmdoc/flucq.doc ). QM/MM Fluctuating Charge Potential* GBorn: (chmdoc/genborn.doc ). Generalized Born Solvation Energy* Genetic: (chmdoc/galgor.doc ). The genetic algorithm commands* Graphx: (chmdoc/graphx.doc ). The graphics subsection for workstations* H-bond: (chmdoc/hbonds.doc ). Generation of hydrogen bonds* H-build: (chmdoc/hbuild.doc ). Construction of hydrogen positions* HQBM: (chmdoc/hqbm.doc ). Biased Molecular Dyanmics* Images: (chmdoc/images.doc ). Use of periodic or crystal environment* Internal: (chmdoc/intcor.doc ). Manipulation of internal coordinates* I/O : (chmdoc/io.doc ). I/O of data structures and files* LonePair : (chmdoc/lonepair.doc). Lone-Pair Facility* LUPOPT : (chmdoc/lupopt.doc ). Low Energy Path OPTimization* MBOND: (chmdoc/mbond.doc ). Multi-body dynamics* MC: (chmdoc/mc.doc ). Monte Carlo simulation program* Minimiz: (chmdoc/minimiz.doc ). Description of the minimization methods* Miscellany: (chmdoc/miscom.doc ). Miscellaneous commands* MMFP: (chmdoc/mmfp.doc ). Miscelaneous Mean Field Potential* Molvib: (chmdoc/molvib.doc ). Molecular vibrational analysis facility* NMR: (chmdoc/nmr.doc ). NMR analysis facility* Non-bonded: (chmdoc/nbonds.doc ). Generation of the non-bonded interaction* Parameters: (chmdoc/parmfile.doc). CHARMM energy parameters* PBEQ: (chmdoc/pbeq.doc ). Poisson-Boltzmann Equation Solver* Perturb: (chmdoc/pert.doc ). Free energy perturbation simulations* Pressure: (chmdoc/pressure.doc). Pressure calculation and usage* Quantum: (chmdoc/qmmm.doc ). Quantum and Molecular Mechanical FF* Replica: (chmdoc/replica.doc ). REPLICA: molecular system replication* RISM: (chmdoc/rism.doc ). Reference Interaction Site Model* SASA: (chmdoc/sasa.doc ). The SASA implicit solvation model* Sbound: (chmdoc/sbound.doc ). Stoichastic boundary* Scalar: (chmdoc/scalar.doc ). Scalar command for atom properties* Select: (chmdoc/select.doc ). Use of the atom selection facility* Structure: (chmdoc/struct.doc ). Structure manipulation (PSF generation)* Substitute: (chmdoc/subst.doc ). Command line substitution parameters* Test: (chmdoc/test.doc ). Commands to test various things* Topology: (chmdoc/rtop.doc ). Residue Topology File* Travel: (chmdoc/travel.doc ). Reaction coordinate refinement command* TSM: (chmdoc/perturb.doc ). Thermodynamic Simulation Method* Umbrella: (chmdoc/umbrel.doc ). Umbrella Sampling* Vibration: (chmdoc/vibran.doc ). Vibrational analysis facility* MMFF: (chmdoc/mmff.doc ). Merck Molecular Force
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