Documentation for c38b2

Frequently used modules

  • Coordinate manipulation and analysis | corman
  • Energy commands | energy
  • Non-bonded options | nbonds
  • Minimization | minimiz
  • Molecular dynamics | dynamc
  • Constraints and restraints | cons
  • Time series and correlation functions | correl
  • Atom selections | select

Modules in alphabetical order

abpo | ace | adumb | afm | analys | apbs | aspenr | aspenrmb | axd | block | cadpac | cca | cff | cfti | changelog | charmm | charmmrate | cheq | commands | cons | consph | corman | correl | corsol | cross | crystl | csa | developer | diesel | dimens | dims | domdec | drude | dynamc | eds | eef1 | emap | energy | ensemble | epmf | ewald | facts | fitcharge | fitparam | flucq | fourd | g09 | galgor | gamess | gamess-uk | gamus | gbim | gbmv | gbsw | genborn | gnn | gpu | graphx | grid | hbonds | hbuild | hqbm | images | install | intcor | io | lonepair | lupopt | mc | mcma | minimiz | miscom | mmff | mmff_params | mmfp | mmpt | mndo97 | molvib | monitor | mscale | mtp | mts | nbonds | nmr | nose | openmm | overlap | parallel | parmfile | pbeq | pdetail | pert | perturb | phmd | pimplem | pipf | pnm | preflx_list | prefx | pressure | primo | proto | qchem | qmmm | qturbo | qub | random | rdfsol | repdstr | replica | rism | rtop | rush | rxncons | sasa | sbound | scalar | sccdftb | scpism | select | sgld | shapes | shell | stringm | struct | subst | support | tamd | test | testcase | tmd | torque | tpcntrl | tps | trek | umbrel | usage | valbond | vibran | zerom

Complete list of modules

  • Adaptively Biased Path Optimization (ABPO) Method | abpo
  • Analytical Continuum Solvent (ACS) Potential | ace
  • Adaptive Umbrella Sampling Module | adumb
  • The AFM Module of CHARMM | afm
  • Analysis Commands | analys
  • Adaptive Poisson-Boltzmann Solver (APBS) | apbs
  • Atomic Solvation Parameter Based Energy | aspenr
  • Atomic Solvation Parameter Model with Implicit Membrane | aspenrmb
  • The AXD Module of CHARMM | axd
  • Partition molecular system into blocks | block
  • Combined Quantum Mechanical and Molecular Mechanics Method | cadpac
  • Common Component Architecture | cca
  • Consistent Force Field (CFF) | cff
  • CFTI: conformational energy/free energy calculations | cfti
  • CHARMM Developer's Change Log | changelog
  • Chemistry at HARvard Macromolecular Mechanics | charmm
  • CHARMM/POLYRATE INTERFACE | charmmrate
  • The CHarge EQuilibration Method | cheq
  • CHARMM commands | commands
  • CONSTRAINTS | cons
  • Monte-carlo method for constant pH simulations | consph
  • The Coordinate Manipulation Commands | corman
  • Correlation Functions | correl
  • Solvent Correlation Functions | corsol
  • Reactive Molecular Dynamics with Surface Crossing | cross
  • Calculations on Crystals using CHARMM | crystl
  • Distributed CSA (Conformational Space Annealing) Command | csa
  • CHARMM Developer Guide | developer
  • Combined Quantum Mechanical and Molecular Mechanics Method | diesel
  • How to set CHARMM to run with any size system | dimens
  • Dynamic Importance Sampling (DIMS) | dims
  • Domain Decomposition | domdec
  • New Drude Oscillator Format | drude
  • Dynamics: Description and Discussion | dynamc
  • Enveloping Distribution Sampling Method | eds
  • Effective Energy Function 1 | eef1
  • The EMAP module | emap
  • Energy Manipulations: Minimization and Dynamics | energy
  • ENSEMBLE averaging / replica exchange | ensemble
  • EPMF Module of CHARMM | epmf
  • The Ewald Summation method | ewald
  • FACTS: Fast Analytical Continuum Treatment of Solvation | facts
  • The Charge and Drude Polarizability Fitting | fitcharge
  • Parameter Fitting Procedure | fitparam
  • Combined QM/MM Fluctuating Charge Potential for CHARMM | flucq
  • 4 Dimension dynamics: Description and Discussion | fourd
  • Combined Quantum Mechanical and Molecular Mechanics Method | g09
  • Galgor: Commands which deal with Genetic Algorithm and Monte Carlo. | galgor
  • Combined Quantum Mechanical and Molecular Mechanics Method | gamess
  • Combined Quantum Mechanical and Molecular Mechanics Method | gamess-uk
  • Gaussian Mixture Adaptive Umbrella Sampling (GAMUS) | gamus
  • Generalized Born Solvation Energy Module with Implicit Membrane | gbim
  • Generalized Born using Molecular Volume (GBMV) | gbmv
  • Generalized Born with a simple SWitching (GBSW) | gbsw
  • Generalized Born Solvation Energy and Forces Module | genborn
  • Genetic Neural Network | gnn
  • Installing and running CHARMM on GPU | gpu
  • GRAPHICS | graphx
  • Grid: A general facility to implment grid-based potentials for docking | grid
  • Generation of Hydrogen Bonds | hbonds
  • Construction of hydrogen positions | hbuild
  • The HQBM Module of CHARMM | hqbm
  • IMAGES | images
  • CHARMM Release and Installation | install
  • The Internal Coordinate Manipulation Commands | intcor
  • Input-Output Commands | io
  • Lone Pair Facility | lonepair
  • Low Energy Path OPTmization | lupopt
  • Monte Carlo | mc
  • Monte Carlo Minimization/Annealing (MCMA) | mcma
  • Energy Manipulations: Minimization and Dynamics | minimiz
  • Miscellaneous Commands | miscom
  • Merck Molecular Force Field (MMFF94) | mmff
  • The MMFF94 Setup Procedure And Parameter Files | mmff_params
  • Miscellaneous mean field potentials | mmfp
  • Molecular Mechanics with Proton Transfer (MMPT) | mmpt
  • Combined Quantum Mechanical and Molecular Mechanics Method | mndo97
  • The MOLVIB Module of CHARMM | molvib
  • Monitor commands: Commands to monitor various dynamics properties | monitor
  • Multi Scale Command: MSCALE | mscale
  • Multipole Module | mtp
  • Multiple Time Scales Method (MTS) | mts
  • Generation of Non-bonded Interactions | nbonds
  • NMR Analysis Module | nmr
  • The documentation of Nose-Hoover method - Masa Watanabe | nose
  • OpenMM GPU acceleration interface to CHARMM | openmm
  • Overlap of Molecular Similarity | overlap
  • Parallel Implementation of CHARMM | parallel
  • CHARMM Emprical Energy Function Parameters | parmfile
  • Poisson-Bolztmann Equation Module | pbeq
  • Details about TSM Free Energy Calculations | pdetail
  • Free Energy Perturbation Calculations | pert
  • Perturbation: Thermodynamic Perturbation Calculations. | perturb
  • Continuous constant pH Molecular Dynamics (PHMD) | phmd
  • Implementation of the Thermodynamic Simulation Method | pimplem
  • Polarizable Intermolecular Potential Functions (PIPF) | pipf
  • Plastic Network Model (PNM) | pnm
  • LIST OF ALL COMPILE (##) KEYWORDS IN CHARMM | preflx_list
  • CHARMM Preprocessing | prefx
  • Constant Pressure/Temperature (CPT) Dynamics | pressure
  • PRIMO Module of CHARMM | primo
  • Prototypes | proto
  • Combined Quantum Mechanical and Molecular Mechanics Method | qchem
  • Combined Quantum and Molecular Mechanical Hamiltonian | qmmm
  • A Quantum Mechanical / Molecular Mechanical (QM/MM) Interface | qturbo
  • Closed and Open Polymer Chain Path-Integral Methods for QM/MM | qub
  • Random Number Generator Controlling Commands | random
  • Radial Correlation Functions | rdfsol
  • The Parallel Distributed Replica | repdstr
  • Replica: Commands which deal with replication of the molecular system: Replica. | replica
  • RISM (Reference Interaction Site Model) module | rism
  • Residue Topology File | rtop
  • RUSH: A simple implicit-solvent force-field for protein simulation | rush
  • Rxncons: Commands for holonomic constrains of different order parameters | rxncons
  • The SASA implicit solvation model | sasa
  • Method and implementation of deformable boundary forces | sbound
  • SCALar : commands to manipulate scalar atom properties | scalar
  • Combined Quantum Mechanical and Molecular Mechanics Method | sccdftb
  • Screened Coulomb Potentials Implicit Solvent Model (SCPISM) | scpism
  • ATOM SELECTION | select
  • Self-Guided Langevin Dynamics (SGLD) | sgld
  • Shape Descriptors | shapes
  • Shell Decomposition | shell
  • 0-K String Method | stringm
  • Generation and Manipulation of the Structure (PSF) | struct
  • Command Line Substitution Parameters | subst
  • Support Programs and Data Files | support
  • Torsion Angle Molecular Dynamics (TAMD) Module | tamd
  • Test commands: Commands to test various conditions in CHARMM | test
  • CHARMM Testcases | testcase
  • Targeted Molecular Dynamics | tmd
  • Manipulating torques: TORQUE | torque
  • Temperature and pressure control | tpcntrl
  • Transition Path Sampling | tps
  • TReK: a program for Trajectory REfinement and Kinematics. | trek
  • Order Parameters | umbrel
  • How to use CHARMM | usage
  • VALBOND-TRANS | valbond
  • Vibration Analysis | vibran
  • The Z Module is a general facility for carrying out conformational | zerom