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c39b1
c39b1
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
/
gopair
/
gpu
/
graphx
/
grid
/
hbonds
/
hbuild
/
hqbm
/
images
/
install
/
intcor
/
io
/
lonepair
/
lupopt
/
mc
/
mcma
/
minimiz
/
miscom
/
mmff
/
mmff_params
/
mmfp
/
mmpt
/
mndo97
/
molvib
/
monitor
/
mrmd
/
mscale
/
mtp
/
mtpl
/
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
Partion 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
Contact Information
CHARMM
/
charmm_development_project@tammy.harvard.edu
Website contents
/
Michael Feig (
feig@msu.edu
)
Website hosting/privacy
/
John Legato (
legatoj@nhlbi.nih.gov
)