Menu Item List
CHARMM c32b2 Menu Item List
| The info menu items for all of the CHARMM .doc files, in a
single document to facilitate searching. |
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
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
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
cons.doc* Harmonic Atom:: "CONS HARM" Hold atoms in place
cons.doc* Dihedral:: "CONS DIHE" Hold dihedrals 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* 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
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
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
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* Checkin:: How to deposit your development version into the
developer.doc* prefx:: 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.
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
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
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
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
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
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
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.
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
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* 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
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
mbond.doc* Substructuring:: How to define bodies
mbond.doc* Modes:: Description of the keywords and options
mbond.doc* Other:: One line MBOND commands
mbond.doc* Dynamics:: Recommended input options and values
mbond.doc* Output:: Output from a dynamics run
mbond.doc* Harmonic:: Body-based modes from Harmonic Poteintial
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* 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
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
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
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* 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* PERT/MMFP:: MMFP in PERT
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
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
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)
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
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* Functionality:: Functionality of the interface code.
qchem.doc* Status:: Status of the interface code.
qmmm.doc* Syntax:: Syntax of QM/MM Commands
qmmm.doc* Description:: Brief Description of Quantum Commands
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
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* 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
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* 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* 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
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 after patches
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
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 requirements.
trek.doc* Usage:: Usage: end-points, QM/MM, fixing atoms, etc.
trek.doc* Input:: Reading initial path, declaring saddle-points.
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* RXNCOR:: Specifying a reaction coordinate in CHARMM
umbrel.doc* Dynamics:: Running dynamics under an umbrella potential
umbrel.doc* Statistics:: Extracting results from umbrella dynamics
umbrel.doc* Results:: Interpreting and using the results
usage.doc* Meta-Syntax:: Describing the Syntax of 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.
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* 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* GANM:: Gaussian(Anisotropic) Network Model