Documentation for c39b2

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

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
The Go pairwise Energy Module of CHARMM | gopair
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-Surface Adiabatic Reactive Molecular Dynamics (MS-ARMD) | mrmd
Multi Scale Command: MSCALE | mscale
Multipole Module | mtp
Spherical Multipole Electrostatic Module using Local | mtpl
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