CHARMM c42b2 Menu Item List

The info menu items for all of the CHARMM .doc files, in a single document to facilitate searching.

abpo.doc* Description::           Introduction and algorithm
abpo.doc* Syntax::                Description of commands and options
abpo.doc* Remarks::               Implementation remarks
abpo.doc* Examples::              Usage examples
abpo.doc* References::            References
ace.doc* Syntax::      Syntax of the ACE specifications
ace.doc* Defaults::    Defaults and Recommended values 
ace.doc* Function::    Purpose of each of the specifications
ace.doc* Examples::    Usage examples of the ACE module
adumb.doc* Syntax::      Syntax of the ADUMB commands
adumb.doc* Function::    Purpose of each of the commands
adumb.doc* Examples::    Usage examples of the ADUMB module
afm.doc* Syntax::              Syntax of the AFM command
afm.doc* Function::            Purpose of each of the keywords
afm.doc* Input::               AFM Input Description
analys.doc* Description::         Description of analysis facility
analys.doc* Energy::              Energy partitioning
apbs.doc* Syntax::      Syntax of the PBEQ commands
apbs.doc* Function::    Purpose of each of the commands
apbs.doc* Examples::    Usage examples of the PBEQ module
aspenr.doc* Syntax::      Syntax of ASP input
aspenr.doc* Structure::   Structure of the .surf file containing ASP data
aspenr.doc* Examples::    Usage examples of the ASP module
aspenrmb.doc* Syntax::      Syntax of ASPENRMB input
aspenrmb.doc* Structure::   Structure of the .surf file containing ASP data
aspenrmb.doc* Examples::    Usage examples of the ASPENRMB module
axd.doc* Syntax::              Syntax of the AXD command
axd.doc* Description::         Description of the command
axd.doc* References::          References
axd.doc* Example::             Usage Example
axd.doc* Comments::            The current status
block.doc* Syntax::              Syntax of the block commands
block.doc* Function::            Purpose of each of the commands
block.doc* Hints::               Some further explanations/hints
block.doc* Limitations::         Some warnings...
cadpac.doc* Description::         Description of the CADPAC commands
cadpac.doc* Using::               How to run CADPAC in CHARMM
cadpac.doc* Installation::        How to install CADPAC in CHARMM environment
cadpac.doc* Status::              Status of the interface code
cca.doc* Description::         Description of the CCA.
cca.doc* Using::               How to use CCA
cca.doc* Installation::        How to install CHARMM with CCA.
cca.doc* Status::              Status of the interface code.
cff.doc* Usage::         How to use CFF with CHARMM standalone
cff.doc* Status::        Current status of CFF implementation in CHARMM
cff.doc* Theory::        Basis for, parameterization and performance of CFF
cff.doc* Funcform::      Functional form of the CFF energy expression
cff.doc* Refs::          References to papers describing CFF
cfti.doc* Constraints::   Note on constrained optimization implementation
cfti.doc* CFTINT::        Description and syntax of standard conformational
cfti.doc* CFTIM::         Description and syntax of multidimensional onformational
changelog.doc* C21-C22::     Modifications of Developmental CHARMM21 to CHARMM22
changelog.doc* C20-C22::     Major enhancements and developments in CHARMM22
changelog.doc* C22-C23::     Major enhancements and developments in CHARMM23
changelog.doc* C23-C24::     Major enhancements and developments in CHARMM24
changelog.doc* C24-C25::     Major enhancements and developments in CHARMM25
charmmrate.doc* Description::         Description of the POLYRATE driver in CHARMM
charmmrate.doc* Usage::               How to run POLYRATE in CHARMM
charmmrate.doc* Installation::        How to install POLYRATE in CHARMM
charmmrate.doc* Status::              Status of the interface code
cheq.doc* Description::      Description of the CHEQ Function
cheq.doc* Syntax::           Syntax of the CHEQ commands
cheq.doc* Options::          CHEQ Command Options
cheq.doc* Energy::           Usage with Energy and Dynamics commands
cheq.doc* Scalar::           Usage with the Scalar Command
cheq.doc* Examples::         Usage Example Script
cheq.doc* Mixed Systems::    Mixed Polarizable / Non-Polarizable Systems (FQ/MM)
cheq.doc* References::       References for CHEQ Methods
cmake.doc* Workflow::      Three Steps to a CMake Install
cmake.doc* Configuration:: The First Step
cmake.doc* Compilation::   The Second Step
cmake.doc* Installation::  The Third and Final Step
cons.doc* Harmonic Atom::       "CONS HARM" Hold atoms in place
cons.doc* Dihedral::            "CONS DIHE" Hold dihedrals near selected values
cons.doc* Puckering::           "CONS PUCK" Hold puckering near selected values
cons.doc* Internal Coord::      "CONS IC"   Holds bonds, angles and
cons.doc* Quartic Droplet::     "CONS DROP" Puts the entire molecule in a cage
cons.doc* RMSD restraints::     "CONS RMSD" Holds atoms in place relative to
cons.doc* EMAP restraints::     "CONS EMAP" Soft restraint to induce a group of atoms 
cons.doc* Fixed Atom::          "CONS FIX"  Fix atoms rigidly (sets the IMOVE array)
cons.doc* Center of Mass::      "CONS HMCM" Constrain center of mass of selected atoms
cons.doc* SHAKE::               "SHAKE"     Fix bond lengths during dynamics.
cons.doc* NOE::                 "NOE"       Impose distance restraints from NOE data
cons.doc* Restrained Distances:: "RESD"     Impose general distance restraints
cons.doc* External Forces::     "PULL"      Impose externally applied (pulling) force
cons.doc* Rg/RMSD restraint::   "RGYR"      Impose radius of gyration or rmsd restraint
cons.doc* Distance Matrix restraint:: "DMCO" Impose a distance matrix restraint
cons.doc* COFM along path::     "CONS PATH" Constrain center of mass along 3D path
cons.doc* Helix Restraint::     "CONS HELI" Impose helix restraint
consph.doc* Introduction::        Overview of the constant pH Monte Carlo method
consph.doc* Syntax::              Syntax of the Constant pH code
consph.doc* Notes::               Usage notes
corman.doc* Syntax::                Syntax of the coordinate manipulations commands
corman.doc* Simple::                Descriptions of the simple commands
corman.doc* Function::              Descriptions of the remaining commands
corman.doc* Substitutions::         Description and usage of substitution values
correl.doc* Syntax::              The syntax of the correlation command
correl.doc* General::             General information regarding the correlation section
correl.doc* Enter::               How to specify time series
correl.doc* Trajectory::          How to reference to trajectory files
correl.doc* Edit::                How the edit the time series specifications
correl.doc* Mantime::             How to manipulate time series
correl.doc* Corfun::              How to generate correlation functions.
correl.doc* Spectrum::            How to get a spectrum from a correlation function
correl.doc* Cluster::             How to cluster time series data into similar groups
correl.doc* IO::                  Input/output guide to correlation functions and series
correl.doc* Examples::            Just what it says
corsol.doc* Syntax::          The syntax of the correlation command
corsol.doc* General::         General information regarding the correlation section
corsol.doc* Enter::           How to specify time series
corsol.doc* Trajectory::      How to reference to trajectory files
corsol.doc* IO::              Input/output guide to correlation functions and series
corsol.doc* Examples::        Just what it says
cross.doc* Syntax::                Syntax of the CROSS command
cross.doc* Description::           Description of the keywords and options
cross.doc* Extra parameter file::  Description of the input format of multiple potential
cross.doc* Special L-J treatment:: Application of unique Lennard-Jones potentials to
crystl.doc* Syntax::             Syntax of the CRYSTAL command
crystl.doc* Function::           A brief description of each command
crystl.doc* Examples::           Sample testcases
crystl.doc* Implementation::     Background and implementation
csa.doc* Syntax::      Suggested syntax
csa.doc* Example::     Sample CHARMM slave script
csa.doc* Notes::       Additional notes
dcor.doc* Commands::            Invoking DCOR
dcor.doc* Background::          An introduction to distance correlation
dcor.doc* References::          Relevant citations
dcor.doc* Example::             Outline of an example input script
denbias.doc* Syntax::              Syntax of the DENBIAS command
denbias.doc* Function::            Purpose of each of the command
denbias.doc* Examples::            Usage examples of the DENBIAS module
developer.doc* Implement::   CHARMM Implementation and Management
developer.doc* Directories:: What directories are used to store what information
developer.doc* Standards::   Standards (rules) for writing CHARMM code
developer.doc* Tools::       Tools for CHARMM developers
developer.doc* Modify::      The procedure for modifying anything in CHARMM
developer.doc* Document::    How to document CHARMM commands and features
developer.doc* API::         How to generate low-level documentation from code
developer.doc* Checkin::     How to deposit your development version into the
developer.doc* (prefx.doc)::  CHARMM Source Code Preprocessor
developer.doc* makemod::      Module Makefiles and Optimization Procedure
diesel.doc* Description::         Description of the gamess commands.
diesel.doc* Using::               How to run GAMESS in CHARMM.
diesel.doc* Installation::        How to install GAMESS in CHARMM environment.
diesel.doc* Status::              Status of the interface code.
diesel.doc* Functionality::       Functionality of the interface code.
dims.doc* Syntax::           Syntax of the DIMS command and related commands.
dims.doc* Description::      Detailed description of DIMS and parameters.
dims.doc* Restrictions::     Restrictions, Known Bugs, and possible pitfalls.
dims.doc* Examples::         Example DIMS invocation and output.
dims.doc* References::       Articles and contact information.
dims.doc* Developer notes::  Notes on compiling Charmm with DIMS and source code
dims.doc* Common DIMS parameters::  Parameters that are always needed for DIMS.
dims.doc* DIMS-NM parameters::      Parameters needed for DBNM with mode
dims.doc* DIMS-NM algorithm::       Description of DIMS-NM.
dims.doc* Progress scores::         How to measure progress along the transition.
dims.doc* Trajectory scores::       How to measure the quality of the trajectory.
dims.doc* Mode self-avoidance::  more on using the 'mode self-avoidance' algorithm
dims.doc* Mode combinatorics::   more on combining modes and how it interacts with 
dims.doc* DIMS-NM algorithm::
dims.doc* Mode self-avoidance file::  Details on the file used to record
dims.doc* RMSD score::                 configuration space root mean square distance
dims.doc* Interatomic distance::
dims.doc* Onsager-Machlup score::      Onsager-Machlup action as a score
dims.doc* DIMS score::                 The (approximated) DIMS score.
dims.doc* NM DIMS example::           Normal modes are used to drive the transition.
dims.doc* DCAR DIMS example::         DIMS-cartesian are used to drive the transition.
dims.doc* NM DIMS + self-avoidance example::  Normal modes and self-avoidance to
dims.doc* TMD last mile example::     Using DIMS-NM and TMD to reach the target.
dims.doc* Choosing parameters::       Initial guidance on how to choose appropriate
dims.doc* DIMS output::               DIMS diagnostics explained.
domdec.doc* Description::    Short description 
domdec.doc* Limitations::    Which features are enabled and which not
domdec.doc* Syntax::         Syntax of the domdec command
domdec.doc* Examples::       Examples of using domdec
domdec.doc* Installing::     Enabling domdec in charmm
drude.doc* Description:: Description of new DRUDE model RTF
drude.doc* Syntax::      Syntax of the DRUDE command
drude.doc* Description:: Description of the DRUDE command
drude.doc* Toppar::      Effect on the topology and parameters
drude.doc* Warnings::    To be aware of when using the DRUDE command
drude.doc* Examples::    Usage examples of the DRUDE command
dynamc.doc* Syntax::              Syntax of the dynamics command
dynamc.doc* Description::         Description of the keywords and options
dynamc.doc* Recommended::         Recommended input options and values
dynamc.doc* Discussion::          Running dynamics
dynamc.doc* Output::              Output from a dynamics run
dynamc.doc* Trajectory::          Trajectory manipulation and I/O
dynamc.doc* Merge::               Merging or breaking up trajectory files into
dynamc.doc* Reorient::            Reorienting a coordinate trajectory
dynamc.doc* RMSDyn::              Computes the RMS difference between two trajectories
dynamc.doc* Format::              formatting and unformatting a dynamics trajectory
dynamc.doc* CVELocity::           Constant velocity dynamics
dynamc.doc* TSALlis::             Molecular dynamics in the Tsallis ensemble
dynamc.doc* CENT::                The reCENTering command
eds.doc* Syntax::              Syntax of the EDS dynamics command
eds.doc* Examples::            EDS usage examples
eds.doc* Notes::               Usage notes and hints
eef1.doc* Syntax::         Syntax of the EEF1 commands
eef1.doc* References::     Useful references    
eef1.doc* Example::        Input file 
emap.doc* Syntax::            Syntax of the EMAP commands
emap.doc* Description::       Description of the EMAP functions
emap.doc* Substitution::      Description of substitution values
emap.doc* Examples::          Usage example of the EMAP commands
energy.doc* Description::         Description of the energy commands
energy.doc* Skipe::               Selection of particular energy terms
energy.doc* Interaction::         Computation of interaction energies and forces.
energy.doc* Fast::                Requirements for using the fast routines
energy.doc* Needs::               Requirements for all energy evaluations
energy.doc* Optional::            Optional actions to be taken beforehand
energy.doc* Substitution::        Command line energy substitution parameters
energy.doc* Running Average::     ESTATS command usage
energy.doc* Multe::               Multiple energy evaluation
ensemble.doc* Syntax::                  Syntax of the ENSEMBLE command
ensemble.doc* General Description::     General info on I/O and other practical matters
ensemble.doc* Replica Exchange::        Using replica exchange to swap between different
ensemble.doc* PINS Method::             Description of the PINS implementation
ensemble.doc* Ensemble Restraints::     Using HQBM and ENSEMBLE to average restraints
ensemble.doc* Force-field Averaging::   Combining two potentials with exponential averaging
ensemble.doc* 0-K String method::       Finding minimum energy paths (MEP) between two
ensemble.doc* Test Cases::              Description of c33 and c34 tests
epmf.doc* Syntax::              Syntax of the EPMF command
epmf.doc* Function::            Purpose of each of the command
epmf.doc* PMF-file::            Format of PMF file
epmf.doc* Examples::            Usage examples of the EPMF module
ewald.doc* Syntax::          Syntax of the Ewald summation specification
ewald.doc* Defaults::        Defaults used in the specification
ewald.doc* Function::        Description of the options
ewald.doc* Discussion::      More general discussion of the algorithm
facts.doc* Description:: Description of FACTS
facts.doc* Syntax::      Syntax of the FACTS Commands
facts.doc* Function::    Description of the FACTS keywords and options
facts.doc* Examples::    Usage examples of the FACTS module
facts.doc* Examples-II:: Usage examples of the FACTS energy decomposition
fitcharge.doc* Syntax::              Syntax of charge fitting commands
fitcharge.doc* Introduction::        Introduction to charge fitting
fitcharge.doc* Function::            Purpose of the commands
fitcharge.doc* Example::             Input example
fitcharge.doc* Limitations::		Known limitations
fitparam.doc* Introduction::        Overview of functionality
fitparam.doc* Syntax::              Syntax of commands
fitparam.doc* Keywords::            Description of keywords
fitparam.doc* Format::              File format
fitparam.doc* Example::             Input examples
fitparam.doc* Limitations::         Known limitations
flucq.doc* Syntax::                Syntax of the FLUCQ command
flucq.doc* Activation::            Starting FlucQ from a CHARMM input file
flucq.doc* Charge solution::       Solving for exact charges
flucq.doc* Reference energy::      Setting the ``zero'' for FlucQ polarisation
flucq.doc* Caveats::               Changes to be aware of; known limitations
flucq.doc* Using FlucQ with QM::   Necessary changes for use with CADPAC or GAMESS
flucq.doc* Examples::              Simple uses of the FLUCQ command
flucq.doc* Implementation::        Mathematical and computational details
fmm.doc* Description::         Description of the OVERLAP commands.
fmm.doc* Usage::               How to use the OVERLAP method.
fmm.doc* Installation::        Installation of the OVERLAP method
fmm.doc* Performance::         Performance Issues
fourd.doc* Syntax::              Syntax of the 4 dimension dynamics command
fourd.doc* Description::         Description of the keywords and options
fourd.doc* Recommended::         Recommended input options and values
fourd.doc* Discussion::          Running 4 dimension dynamics
fourd.doc* Output::              Output from a 4 dimension dynamics run
fren.doc* Syntax::              Syntax of the FREN command
fren.doc* Examples::          FREN usage examples
fren.doc* Notes::               Usage notes and hints
g09.doc* Description::            Description of the GAUS commands.
g09.doc* Usage::                  How to run Gaussian09 in CHARMM.
galgor.doc* Implementation::      A brief description of the anatomy of GA
galgor.doc* Syntax::              Syntax of the replication commands
galgor.doc* Description::         Description of key words and commands usage
galgor.doc* Restrictions::        Restrictions on usage
galgor.doc* Examples::            Supplementary examples of the use of GA
gamess.doc* Description::         Description of the gamess commands.
gamess.doc* Using::               How to run GAMESS in CHARMM.
gamess.doc* Replica path::        How to run GAMESS/CHARMM with REPLICA/PATH.
gamess.doc* Installation::        How to install GAMESS in CHARMM environment.
gamess.doc* Status::              Status of the interface code.
gamess.doc* Functionality::       Functionality of the interface code.
gamess.doc* Implementation::      Implementation.
gamess-uk.doc* Description::         Description of the gamess commands.
gamess-uk.doc* Using::               How to run GAMESS in CHARMM.
gamess-uk.doc* Installation::        How to install GAMESS in CHARMM environment.
gamess-uk.doc* Status::              Status of the interface code.
gamus.doc* Syntax::        Syntax of the GAMUS commands
gamus.doc* Function::      Purpose of each of the commands
gamus.doc* Caveats::       Some limitations of the GAMUS method
gamus.doc* Installation::  Installation of GAMUS within CHARMM
gamus.doc* Examples::      Usage example of the GAMUS module
gbim.doc* Syntax::      Syntax of the GBIM commands
gbim.doc* Function::    Purpose of each of the commands
gbim.doc* Examples::    Usage examples of the GBIM module
gbmv.doc* Description:: Description of GBMV and related commands
gbmv.doc* Syntax::      Syntax of the GBMV Commands
gbmv.doc* Function::    Purpose of each of the commands
gbmv.doc* Examples::    Usage examples of the GBMV module
gbsw.doc* Description:: Description of GBSW and related commands
gbsw.doc* Syntax::      Syntax of the GBSW Commands
gbsw.doc* Function::    Purpose of each of the commands
gbsw.doc* Examples::    Usage examples of the GBSW module
genborn.doc* Syntax::      Syntax of the GBORN Commands
genborn.doc* Function::    Purpose of each of the commands
genborn.doc* Examples::    Usage examples of the GBORN module
gnn.doc* Syntax::           Syntax required to invoke GNN
gnn.doc* Description::      Description of GNN specific keywords
gnn.doc* Examples::         Examples
gnn.doc* References::       References
gopair.doc* Syntax::              Syntax of the GoPair command
gopair.doc* Function::            Purpose of each of the keywords
gopair.doc* Example::             Example input setup
gpu.doc* Syntax::              Syntax of the nonbond specification
gpu.doc* Installation::        How to install GPU version of CHARMM.
gpu.doc* Parallel::            A variety of parallel setups by PARA GPUS ...
graphx.doc* Summary::       Syntax and Command Summary
graphx.doc* Description::   Detailed Command Description with Examples
graphx.doc* Output::        PostScript, FDAT, LIGHT, and POV-Ray file formats
graphx.doc* Addendum::      X11 Usage and Compiling Tips, Other Useful Programs
grid.doc* Implementation::      A brief description of the anatomy of the module
grid.doc* Syntax::              Syntax of the commands
grid.doc* Description::         Description of key words and commands usage
grid.doc* Restrictions::        Restrictions on usage
grid.doc* Examples::            Supplementary examples of the use of the module
hbonds.doc* Syntax::              Syntax of the Hydrogen bond specification
hbonds.doc* Function::            Purpose of each of the keywords
hbuild.doc* Syntax::              Syntax of the HBUILD command
hbuild.doc* Algorithm::           Description of the used algorithm
hqbm.doc* Syntax::              Syntax of the HQBM command
hqbm.doc* Function::            Purpose of each of the keywords
hqbm.doc* Input::               HQBM Input Description
images.doc* Read::                Description of the IMAGE data file.
images.doc* Write::               The write and print options regarding images.
images.doc* Update::              Options and description of the image update.
images.doc* Patching::            Specification of image patching.
images.doc* Centering::           Secification of image centering during updates.
images.doc* Operation::           Some details and requirements for operation
images.doc* MIPB::                Minimum Image Periodic Boundary (simple)
install.doc* Contents::      List of Contents of the current release
install.doc* Machines::      Machines supported
install.doc* Install::       Installation Procedure
install.doc* Documentation:: CHARMM Documentation via emacs INFO program
install.doc* TOPPAR::        Standard CHARMM Topology and Parameter Files
install.doc* UserForm::      CHARMM User Group support
intcor.doc* Syntax::              Syntax of the internal coordinate commands
intcor.doc* Function::            Purpose of each of the commands
intcor.doc* Structure::           Description of the structure of internal coordinates
io.doc* Read::        Reading data from external sources
io.doc* Write::       Writing data structures in machine readable form
io.doc* Print::       Writing data structures in a human readable form on unit 6
io.doc* Titles::      Specifying and manipulating titles
io.doc* IOFORM::      Specify PSF file format
io.doc* Read Syntax::            Syntax of the READ command
io.doc* Segments::               Reading segments'sequences and coordinates
io.doc* Sequence::               Reading a segment's sequence
io.doc* Coordinate::             Reading coordinates
io.doc* Universal::              Reading coordinates from nonstandard formats
io.doc* Param Files::            The formats used in parameter files
io.doc* RTF File format::        The format used in topology files
io.doc* Other files::            Reading all other file types
larmord.doc* Syntax::              Syntax of the LARMORD  command
larmord.doc* Background::          Description of LARMORD methods
larmord.doc* Examples::            LARMORD usage examples
lonepair.doc* Syntax::                 Syntax of the lone-pair command
lonepair.doc* Description::            Description of the lone-pair facility
lupopt.doc* Syntax::             Syntax of the LUPOpt command
lupopt.doc* Description::        Description of the keywords and options for
lupopt.doc* Memory::             Memory Requirements
mc.doc* Syntax::              Syntax of MOVE and MC commands
mc.doc* Description::         Description of MOVE and MC commands
mc.doc* Examples::            Examples of MOVE and MC commands
mc.doc* SA-MC simulations::   How to use the SA-MC algorithm with this module
mc.doc* Data Structures::     Data structures shared by the MOVE and MC commands
mc.doc* Shortcomings::        Known problems and limitations
mc.doc* References::          Some references of use
mcma.doc* Syntax::         Syntax of the MCMA commands
mcma.doc* Assumptions::    Restrictions inherent in the current implementation 
mcma.doc* Example::        Input file 
mcma.doc* References::     References    
minimiz.doc* Syntax::              Syntax of the energy manipulation commands
minimiz.doc* Description::         Description of the various keyword functions
minimiz.doc* Discussion::          Discussion of the various methods
miscom.doc* Syntax::              Syntax of the miscellaneous commands
miscom.doc* Function::            Purpose of each of the commands
mmff.doc* Usage::         How to use MMFF with CHARMM standalone
mmff.doc* Quanta::        How to use MMFF from QUANTA
mmff.doc* Status::        Current status of MMFF implementation in CHARMM
mmff.doc* Theory::        Basis for, parameterization and performance of MMFF94
mmff.doc* Funcform::      Functional form of the MMFF energy expression
mmff.doc* Refs::          References to papers describing MMFF94
mmff_params.doc* MMFFSYMB::     The MMFFSYMB.PAR file (symbolic atom types)
mmff_params.doc* MMFFAROM::     The MMFFAROM.PAR file (aromatic atom types)
mmff_params.doc* MMFFHDEF::     The MMFFHDEF.PAR file (atom types for hydrogens)
mmff_params.doc* MMFFDEF::      The MMFFDEF.PAR  file (numeric atom types)
mmff_params.doc* MMFFPROP::     The MMFFPROP.PAR file (properties of MMFF atom types)
mmff_params.doc* MMFFBOND::     The MMFFBOND.PAR file (bond-stretching parameters)
mmff_params.doc* MMFFBNDK::     The MMFFBNDK.PAR file (empirical-rule bond parameters)
mmff_params.doc* MMFFANG::      The MMFFANG.PAR  file (angle-bending parameters)
mmff_params.doc* MMFFSTBN::     The MMFFSTBN.PAR file (stretch-bend parameters)
mmff_params.doc* MMFFDFSB::     The MMFFDFSB.PAR file (empirical-rule str-bend parameters)
mmff_params.doc* MMFFOOP::      The MMFFOOP.PAR  file (out-of-plane bending parameters)
mmff_params.doc* MMFFTOR::      The MMFFTOR.PAR  file (torsion partameters)
mmff_params.doc* MMFFVDW::      The MMFFVDW.PAR  file (van der Waals parameters)
mmff_params.doc* MMFFCHG::      The MMFFCHG.PAR  file (bond-increment "charge" parameters)
mmff_params.doc* MMFFPBCI::     The MMFFPBCI.PAR file (empirical-rule charge paramters)
mmff_params.doc* MMFFSUP::      The MMFFSUP.PAR  file (supplementary MMFF parameters)
mmfp.doc* Syntax::                Syntax of the MMFP commands
mmfp.doc* Details::               Descriptions of the GEO subcommands
mmfp.doc* Examples::              Examples of GEO subcommands
mmfp.doc* Substitutions::         Description and usage of substitution values
mmpt.doc* Syntax::                SYNTAX OF MMPT COMMAND
mmpt.doc* Input files::           MMPT INPUT FILES 
mmpt.doc* Limitations::           LIMITATIONS
mndo97.doc* Description::         Description of the MNDO97 commands
mndo97.doc* Usage::               How to run MNDO97 in CHARMM
mndo97.doc* NEWD::                NEWD Command
mndo97.doc* Installation::        How to install MNDO97 in CHARMM environment
molvib.doc* Syntax::              Syntax of the MOLVIB command
molvib.doc* Function::            Purpose of each of the keywords
molvib.doc* Input::               MOLVIB Input Description
monitor.doc* Syntax::              Syntax of the Monitor commands
monitor.doc* Properties::          Description of the properties monitored
mrmd.doc* Syntax::                
mrmd.doc* Description::           
mrmd.doc* Parameter file::         
mrmd.doc* States::
mrmd.doc* Nonbonded::
mrmd.doc* Bonded::
mrmd.doc* Output::                   
mrmd.doc* Example::
mrmd.doc* Troubleshooting::
mrmd.doc* Code::
mscale.doc* Syntax::              Syntax of the mscale specification
mscale.doc* REPDSTR::             Notes to run the MSCAle command with REPDSTR
mscale.doc* Examples::            Examples to run the MSCAle command
mscale.doc* Notes::               Notes abot the MSCAle command
ms-evb.doc* Syntax::                  Syntax of the ENSEMBLE EVB command
ms-evb.doc* General Description::     General info on I/O and other practical matters
ms-evb.doc* Test Cases::              Description of c41 tests
mtp.doc* Interaction::           INTERACTION TYPES INCLUDED
mtp.doc* Input::                 MTP INPUT FILES
mtp.doc* Parameters::            HOW TO OBTAIN ATOMIC MULTIPOLE PARAMETERS
mtp.doc* Gradients::             GRADIENTS
mtp.doc* Potentials::            COMBINATION WITH ANHARMONIC BOND POTENTIALS
mtpl.doc* Coefficients::          MTP coefficients
mtpl.doc* Syntax::                Syntax of the MTPL command
mtpl.doc* Description::           Description of the keywords and options
mtpl.doc* Notes::                 General notes
mts.doc* Syntax::        Syntax of the MTS dynamics command
mts.doc* Desc::          Description of the keywords and options
mts.doc* Note::          Energy routines and MTS method selections 
mts.doc* Exam::          Example of Multiple Time Scale Method
nbonds.doc* Syntax::              Syntax of the nonbond specification
nbonds.doc* Defaults::            Defaults used in the nonbond specification
nbonds.doc* Function::            Description of the options
nbonds.doc* Tables::              Using nonbond lookup tables in place of analytic
nbonds.doc* Cubes::               Alternative way to compute the nonbonded ontact list
nbonds.doc* Cluster::             Cube-Cluster nonbonded list generation method
nmr.doc* Syntax::      Syntax of the NMR commands
nmr.doc* Function::    Purpose of each of the commands
nmr.doc* Examples::    Usage examples of the NMR analysis commands
nose.doc* Syntax::     Syntax of the Nose-Hoover command
nose.doc* Main::       Nose-Hoover method main commands and descriptions
nose.doc* Exam::       Example of Nose-Hoover Method
nwchem.doc* Description::         Description of the NWCHem commands.
nwchem.doc* Using::               How to run NWChem in CHARMM.
nwchem.doc* Replica path::        How to run NWChem/CHARMM with REPLICA/PATH.
nwchem.doc* Installation::        How to install NWChem in CHARMM environment.
nwchem.doc* Status::              Status of the interface code.
nwchem.doc* Functionality::       Functionality of the interface code.
nwchem.doc* Implementation::      Implementation.
openmm.doc* Setup::               Setting up to use/compile CHARMM/OpenMM
openmm.doc* Usage::               Usage and functional support of CHARMM/OpenMM
openmm.doc* Multi-GPU::           Using multiple GPUs and platforms
openmm.doc* Examples::            Examples of CHARMM/OpenMM usage
overlap.doc* Description::         Description of the OVERLAP commands.
overlap.doc* Usage::               How to use the OVERLAP method.
overlap.doc* Implementation::      Implementation of the OVERLAP method
overlap.doc* Performance::         Performance Issues
parallel.doc* Syntax::        Syntax for PARAllel command
parallel.doc* Installation::  Installing CHARMM on parallel systems
parallel.doc* Running::       Running CHARMM on parallel systems
parallel.doc* PARAllel::      Command PARAllel controls parallel communication
parallel.doc* Status::        Parallel Code Status (as of September 1998)
parallel.doc* Using PVM::     Parallel Code implemented with PVM
parallel.doc* Implementation:: Description of implementation of parallel code
parmfile.doc* Overview::      Overview of CHARMM parameter file
parmfile.doc* Multiple::      Rules for the use of multiple dihedrals in CHARMM22
parmfile.doc* Conversion::    Rules for conversion of old nucleic acid rtf and
parmfile.doc* PARMDATA::      Description of Parameter Files available for general use.
pbeq.doc* Syntax::      Syntax of the PBEQ commands
pbeq.doc* Function::    Purpose of each of the commands
pbeq.doc* Examples::    Usage examples of the PBEQ module
pdetail.doc* Introduction::           What will be covered.
pdetail.doc* Theory and Methodology:: General discussion.
pdetail.doc* Practice::               How to do it.
pdetail.doc* Chemical::   Chemical Perturbation Theory and Methodology
pdetail.doc* Internal::   Internal Coordinate Perturbation Theory and Methodology
pdetail.doc* References:: Some References on Thermodynamic Perturbation
pdetail.doc* CPrac::  Chemical Perturbation Practice
pdetail.doc* IPrac::  Internalal Coordinate Perturbation Practice
pdetail.doc* SetUp::     Setting Up the FES Simulation and Running Dynamics
pdetail.doc* PostD::      Post-processing the Data
pdetail.doc* Optional::  Using Some Optional FES Set Up Commands
pdetail.doc* SLOWG::      Slow Growth Method
pdetail.doc* DONT::       The DONT Command
pdetail.doc* UmSam::      Umbrella Sampling in TSM
pert.doc* Syntax::           Syntax of PERT Commands
pert.doc* Description::      Description of PERT Commands
pert.doc* Restrictions::     Restrictions in PERT Command usage
pert.doc* References::       References regarding Free Energy Perturbations
pert.doc* Examples::         A Sample Input Files
pert.doc* Constraints::      Special considerations regarding SHAKE
pert.doc* WHAM::
pert.doc* PERT/PSSP::        Background on the use of soft core potentials (PSSP)
pert.doc* PATCH::
pert.doc* PERT/MMFP::        MMFP in PERT
pert.doc* CHEMical PERT::    Easier setup of alchemical simulations of "chemical paths"
pert.doc* LRCorrection::     Preliminary support of LJ long-range corrections
perturb.doc* Syntax::              Syntax of the set up of the perturbation command.
perturb.doc* Description::         Description of the keywords and options for
perturb.doc* Post-processing::     How to process the perturbation output of the
perturb.doc* ChemPert::    Chemical Perturbation
perturb.doc* ICPert::      Internal Coordinate Perturbation
perturb.doc* PSyn::       Syntax for setting up the post-processing
perturb.doc* PPost::      Description of the keywords and options for setting up
perturb.doc* PProc::      Processing perturbation data
perturb.doc* PEnd::       The END command of post-processing
phmd.doc* Description:: Description of the PHMD Commands
phmd.doc* Syntax::      Syntax of the PHMD Commands
phmd.doc* Function::    Purpose of each of the commands
phmd.doc* Format::      Format of parameter file and how to obtain it
phmd.doc* Examples::    Usage examples of the PHMD module
pimplem.doc* Description::        How Chemical Perturbation works.
pimplem.doc* File Formats::       Output File Formats for Chemical Perturbation.
pimplem.doc* IC Implementation::  Implementation and File Formats for Internal
pipf.doc* Description::      Description of the PIPF Function
pipf.doc* Syntax::           Syntax of the PIPF commands
pipf.doc* Options::          PIPF Command Options
pipf.doc* Examples::         Usage Example Script
pipf.doc* Installation::     How to install PIPF in CHARMM environment.
pipf.doc* Status::           Status of the PIPF code
pipf.doc* References::       References for the PIPF Method
pnm.doc* Description::      Description of the PNM method
pnm.doc* Syntax::           Syntax of the PNM commands
pnm.doc* Options::          Command-line Options
pnm.doc* Examples::         Usage examples
pnm.doc* Installation::     Compiling CHARMM with PNM
pnm.doc* Status::           Status of the code
pnm.doc* References::       References
preflx_list.doc* Include::     Include File Directory
preflx_list.doc* Platform::    Machine Type
preflx_list.doc* OS::          Operating System
preflx_list.doc* Size::        Size Directive
preflx_list.doc* Archi::       Machine Architecture
preflx_list.doc* Parallel::    Parallel CHARMM descriptors
preflx_list.doc* Feature::     Feature Directives
preflx_list.doc* Graphics::    Graphics Directives
preflx_list.doc* Unnorm::      Keywords not for normal use
preflx_list.doc* NOINC::       Major Blocks that can be Removed
preflx_list.doc* Control::     Control Directives
preflx_list.doc* Unknown::     Undocumented keywords (must done soon)
prefx.doc* Conditional:: Conditional compilation directives
prefx.doc* Listing::     Keyword listing directives
prefx.doc* Expansion::   Code expansion directives
prefx.doc* Reserved::    Preprocessor reserved words
prefx.doc* Keywords::    Some important keywords
pressure.doc* Syntax::              Syntax of the CPT dynamics command
pressure.doc* Description::         Description of the keywords and options
pressure.doc* Notes::               Other points to be noted
pressure.doc* Examples::            Isotropic and interfacial systems; constant tensor
pressure.doc* Pressure::            The pressure command
primo.doc* Syntax::              Syntax of the PRIMO command
primo.doc* Function::            Purpose of each of the command
primo.doc* Examples::            Usage examples of the PRIMO module
proto.doc* Syntax::              The syntax of the PROTo commands
proto.doc* General::             General overview
proto.doc* Define::              Defining a new Prototype
proto.doc* Remove::              Delete a prototype
proto.doc* Image::               Adding image prototypes to the list
proto.doc* Info::                Printing prototype information
proto.doc* Caveats::             Some limitations/todos to keep in mind
proto.doc* Examples::
qchem.doc* Description::            Description of the qchem commands.
qchem.doc* Usage::                  How to run Q-Chem in CHARMM.
qchem.doc* Installation::           How to install Q-Chem in CHARMM environment.
qchem.doc* Status::                 Status of the interface code.
qchem.doc* Functionality::          Functionality of the interface code.
qchem.doc* RPath::                  Replica Path Command
qchem.doc* Pert::                   ab inition QM/MM free energy perturbation
qchem.doc* Normal Mode Analysis::   Full QM/MM Normal Mode Anal. through VIBRAN
qchem.doc* Microiterations::        QM/MM Microiteration optimizations 
qchem.doc* MMQM::                   Write internal / external Q-Chem input file
qchem.doc* PCM::                    Specifications for QM/MM/PCM with Q-Chem
qmmm.doc* Syntax::         Syntax of QM/MM Commands
qmmm.doc* Description::    Brief Description of Quantum Commands
qmmm.doc* GLINK::          GHO Method and GLNK Command
qmmm.doc* DECO::           DECO Command
qmmm.doc* DAMP::           DAMP Command
qmmm.doc* PERT::           PERT Command
qmmm.doc* pBOUNd::         Simple Periodic Boundary Condition
qmmm.doc* GROUp::          GROUp keyword
qmmm.doc* CHDYn::          CHDYn keyword
qmmm.doc* NEWD::           NEWDS Command
qmmm.doc* EXTE::           EXTErnal File Command
qmmm.doc* LEPS::           LEPS Command
qmmm.doc* SVB::            SVB Command
qmmm.doc* 2DSVB::          2D Usage of SVB
qmmm.doc* SQUANTUM::       SQUANTUM Module
qmmm.doc* SQM_Syntax::     Syntax of the SQUANTM commands
qmmm.doc* SQM_Install::    Installation of SQUANTM in CHARMM environment
qturbo.doc* Description::            Description of the qturbo commands.
qturbo.doc* Usage::                  How to run TURBOMOLE in CHARMM.
qturbo.doc* Installation::           How to compile CHARMM with the TURBOMOLE interface.
qub.doc* Syntax::         Syntax of QUB Commands
qub.doc* Examples::       Input Examples
random.doc* Syntax::              Syntax of the random command
random.doc* Function::            Purpose of each of the flags and parameters
rdc.doc* Syntax::   Syntax of RDC restraint module
rdc.doc* Details::  Details of RDC commands
rdc.doc* Example::  Examples for RDC restraints
rdfsol.doc* Syntax::              The syntax of the RDFSOL command
rdfsol.doc* General::             General overview
rdfsol.doc* Sets::                Set selections
rdfsol.doc* Limit::               Locally limiting sets in each frame
rdfsol.doc* Options::             other general options
rdfsol.doc* Traj::                Trajectory specifications
rdfsol.doc* Caveats::             Some limitations/todos to keep in mind
rdfsol.doc* Examples::            Just what it says
repdstr.doc* Syntax::              Syntax of the REPD command
repdstr.doc* I/O::                 Input and output functionality
repdstr.doc* FAST::                Usage of FAST replica exchange
repdstr.doc* Examples::            Examples to show the possibilities
repdstr.doc* Output::              Explanation of the replica exchange printout
replica.doc* Syntax::		Syntax of the replication commands
replica.doc* Usage::	 	Description of command usage
replica.doc* Implementation::	A brief description of the anatomy of replication 
replica.doc* Restrictions:: 	Restrictions on usage	
replica.doc* Examples:: 		Supplementary examples of the use of REPLica
replica.doc* Path::                Replica Path Method
replica.doc* OffPath::             Off-Path Optimzation / Simulation 
replica.doc* Pathint::             Path Integral Calculation using REPLica
rism.doc* Syntax::         Syntax of  the RISM commands
rism.doc* Commands::       Explanation of the commands
rism.doc* Theory::         A brief introduction to the RISM theory
rism.doc* References::     Useful references    
rism.doc* Examples::       Input files 
rtop.doc* Overview::      Overview of CHARMM Topology File
rtop.doc* RTFDATA::       Description of Topology Files available for general use
rush.doc* Overview::     Overview of the steps involved in applying the force field
rush.doc* Syntax::       Syntax of the RUSH command
rush.doc* Description::  Description of the RUSH command
rush.doc* Restrictions:: Restrictions on usage
rush.doc* Notes::        Implementation and usage notes
rush.doc* Examples::     Usage examples
rxncons.doc* Syntax::		Syntax of the rxncons commands
rxncons.doc* Usage::	 	Description of command usage
rxncons.doc* Implementation::	A brief description of the anatomy of RCONstraint
rxncons.doc* Restrictions:: 	Restrictions on usage	
rxncons.doc* Examples:: 		Supplementary examples of the use of RCONstraint
sasa.doc* Syntax::         Syntax of the SASA command
sasa.doc* References::     Useful references    
sasa.doc* Example::        Input file 
sbound.doc* Syntax::                             Syntax for all the SBOUnd commands
sccdftb.doc* Description::         Description of the sccdftb commands.
sccdftb.doc* Usage::               How to run sccdftb in CHARMM.
sccdftb.doc* Installation::        How to install sccdftb in CHARMM environment.
sccdftb.doc* FEP::                 Free energy perturbations with SCC-DFTB/MM
sccdftb.doc* Electrostatics::      Electrostatics in SCC-DFTB/MM
sccdftb.doc* GLNK::                GLNK Commands
sccdftb.doc* Status::              Status of the interface code.
scpism.doc* Syntax::         Syntax of the SCPISM commands
scpism.doc* Background::     An introduction to the SCPISM (see also URL)
scpism.doc* References::     Useful references (see URL)    
scpism.doc* Example::        Input file 
select.doc* Syntax::              Syntax of the sequential selection
select.doc* Double::              Double atom selections
select.doc* Function::            Descriptions of the various sequential options
sgld.doc* Syntax::              Syntax of the SGLD dynamics command
sgld.doc* Background::          Description of SGMD/SGLD methods
sgld.doc* Examples::            SGLD usage examples
shell.doc* Syntax::              The syntax of the SHELL command
shell.doc* General::             General overview
shell.doc* Setup::               Setup of overall SHELL parameters
shell.doc* Update::              Decomposing the current coordinates
shell.doc* Define::              Putting shell information into defines
shell.doc* Statistics::          Printing shell information
shell.doc* Off::                 Turning SHELL off
shell.doc* Correl::              CORREL series using the SHELL module
shell.doc* Caveats::             Some limitations/todos to keep in mind
shell.doc* Efficiency::          Things to consider regarding speed
shell.doc* Examples::            Just what it says
ssnmr.doc* 15N Chemical shift : Syntax           ::   Syntax of 15N chemical shift
ssnmr.doc* 15N Cheimical shift : Charmm input    ::   Example of 15N chemical shift 
ssnmr.doc* 15N-1H dipolar coupling: Syntax       ::   Syntax of 15N-1H dipolar coupling 
ssnmr.doc* 15N-1H dipolar coupling: Charmm input ::   Example of 15N-1H dipolar coupling 
stringm.doc* Description::           Introduction to the string method suite
stringm.doc* Invocation::            String method invocation
stringm.doc* SM0K::                  String method at zero temperature
stringm.doc* SMCV::                  String method in collective variables
stringm.doc* FTSM::                  Finite-temperature string method
stringm.doc* Supporting files::      Test cases and supporting files
stringm.doc* References::            References
struct.doc* Generate::            Generating a segment
struct.doc* Nbx::                 Nonbond exclusion lists
struct.doc* Patch::               Multi purpose patch command to modify the PSF
struct.doc* Autogen::             Autogenerate angles and/or dihedrals and activate Drude particles
struct.doc* Delete::              Deleting atoms from the PSF
struct.doc* Rename::              Renaming atoms, residues, or segments
struct.doc* Join::                Joining two adjacent segments to form one
support.doc* Boundary::        Deformable boundary potential files
support.doc* IMTRAN::          Image transformation files
support.doc* NUCS::            Solvation electr. screening by Non-Uniform Charge Scaling
tamd.doc* Syntax::      Syntax of the TAMD commands
tamd.doc* Function::    Purpose of each of the commands
tamd.doc* Examples::    Usage examples of the TAMD analysis commands
testcase.doc* Overview::            Notes about testcases
testcase.doc* Instruction::         How to run testcases
testcase.doc* C20TEST::             Description of testcases in c20test
testcase.doc* C22TEST::             Description of testcases in c22test
testcase.doc* C23TEST::             Description of testcases in c23test
testcase.doc* C24TEST::             Description of testcases in c24test
testcase.doc* C25TEST::             Description of testcases in c25test
testcase.doc* C26TEST::             Description of testcases in c26test
testcase.doc* NBONDTEST::           Description of testcases in cnbondtest
testcase.doc* MMFFTEST::            Description of testcases in cmmfftest
testcase.doc* GRAFTEST::            GRAPHICS Testcases
tmd.doc* Syntax::              Syntax of the dynamics command
tmd.doc* Description::         Description of the keywords and options
tpcntrl.doc* Syntax::       Syntax of the TPCONTROL command
tpcntrl.doc* Description::  Description of the TPCONTROL command
tpcntrl.doc* Dynamics::     Molecular dynamics with TPCONTROL
tpcntrl.doc* Examples::     Usage examples of the TPCONTROL command
tps.doc* Syntax::              Syntax required to invoke TPS
tps.doc* Description::         Description of TPS specific keywords
tps.doc* References::          Some references of use
trek.doc* Syntax::              Syntax of the TReK program.
trek.doc* MainCmd::             Main TREK command and initial setup.
trek.doc* Usage::               Usage: end-points, QM/MM, fixing atoms, etc.
trek.doc* Input::               Reading initial path, declaring saddle-points.
trek.doc* Initialpath::         Create initial path by interpolating sidechains in IC.
trek.doc* CPRcmd::              Conjugate Peak Refinement (CPR) command.
trek.doc* Output::              Saving the path & restart-file, analyzing path.
trek.doc* Tools::               In/De/creasing the number of path-points, miscellaneous
trek.doc* SCMcmd::              Synchronous Chain Minimization (SCM) command.
trek.doc* SDPcmd::              Steepest Descent Path (SDP) and CROS commands.
trek.doc* Bugs::                Known Bugs.
umbrel.doc* Syntax::       Syntax of RXNCOR and its subcommands
umbrel.doc* Examples::     Examples of specifying a reaction coordinate in CHARMM and
usage.doc* Starting CHARMM::     Unix command line arguments
usage.doc* CHARMM Size::         Configuring CHARMM size from a CHARMM script
usage.doc* Meta-Syntax::         Describing the Syntax of Charmm Script Commands
usage.doc* Command Syntax::      Rules for composing command input files.
usage.doc* Run Control::         Ways to modify control flow and stream switching.
usage.doc* I/O Units::           Correspondence between files and unit numbers
usage.doc* AKMA::                Units of Measurement used in CHARMM
usage.doc* Data Structures::     Data Structures used by CHARMM
usage.doc* Standard Files::      Descriptions of parameters, topologies, and
usage.doc* Examples::            Sample runs
usage.doc* Interface::           How to make your own private version of CHARMM
usage.doc* Syntactic Glossary::  Glossary of syntactic terms
usage.doc* Glossary::            Glossary of non-syntactic terms.
valbond.doc* Syntax::              Syntax of the VALB command
valbond.doc* RTF::                 Notes about the RTF
valbond.doc* Hybridization::       Hybridization for transition metals
valbond.doc* Caveats::             Caveats
valbond.doc* References::          References for VALBOND-TRANS
vibran.doc* Syntax::              Syntax of the VIBRan command and all commands
vibran.doc* Normal modes::        Description of normal modes
vibran.doc* I/O::                 Description of the read and write commands.
vibran.doc* Diagonalization::     Description of the diagonalization command.
vibran.doc* Quasiharmonics::      Description of the quasiharmonics command.
vibran.doc* Reduce::              Reduced basis normal mode analysis
vibran.doc* Dimb::                Iterative diagonalization (DIMB).
vibran.doc* Explore::             Command to explore the energy hypersurface
vibran.doc* Fluctuations::        Description of the fluctuation command.
vibran.doc* Princ-Axis-Flucts::   Description of the PAFL command.
vibran.doc* Projections::         Description of the projection command.
vibran.doc* Optimize::        Perform a minimization (and calculate free energy change)
vibran.doc* Mode-definition::     What vectors may be specified
vibran.doc* Rayleigh::            Compute Rayleigh quotients for selected modes
vibran.doc* PED::                 Compute Potential Energy Distribution for a mode
vibran.doc* Edit::                Description of the edit facility.
vibran.doc* Basis::               Generate entire basis sets.
vibran.doc* Fill::                Description of the fill command.
vibran.doc* Second derivatives::  Generation, storage, and uses of second derivatives
vibran.doc* Block::               Block Normal Mode method(BNM).
vibran.doc* MBH::                 Mobile Block Hessian method (MBH).
vibran.doc* GANM::                Gaussian(Anisotropic) Network Model
vibran.doc* VSA::                 Vibrational Subsystem Analysis 
zerom.doc* Method::        Z Method
zerom.doc* Syntax::        Syntax of the ZMOD command
zerom.doc* Description::   Description of the various subcommand functions
zerom.doc* Examples::      Usage examples
zerom.doc* Supplementary:: More complex searches

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