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| 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 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 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 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 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* Fixed Atom:: "CONS FIX" Fix atoms rigidly (sets the IMOVE array) 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 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 eef1.doc* Syntax:: Syntax of the EEF1 commands eef1.doc* References:: Useful references eef1.doc* Example:: Input file 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 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 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* Installation:: How to install GAMESS in CHARMM environment. gamess.doc* Status:: Status of the interface code. gamess.doc* Functionality:: Functionality of the interface code. 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 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 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* 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 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 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 by A. D. Mackerell Jr. 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 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 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 qmmm.doc* Syntax:: Syntax of QM/MM Commands qmmm.doc* Description:: Brief Description of Quantum Commands 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 sbound.doc* Syntax:: Syntax for all the SBOUnd commands select.doc* Syntax:: Syntax of the sequential selection select.doc* Double:: Double atom selections select.doc* Function:: Descriptions of the various sequential options 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 travel.doc* Syntax:: Syntax of the TRAVel command travel.doc* MainCmd:: TRAVel main command and miscellaneous subcommands travel.doc* TrajManip:: TRAVel TRAJectory subcommand (input/output/analysis) travel.doc* CPRcmd:: TRAVel CPR subcommand description travel.doc* SDPcmd:: TRAVel CROS and SDP subcommand description travel.doc* SCMcmd:: TRAVel SCM subcommand description travel.doc* Usage:: TRAVEL Usage Note 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* Optimization:: Optimize parameter set to fit spectra
CHARMM Documentation / chmgr@tammy.harvard.edu