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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 pdetail.doc *Note Theory and Methodology::. The syntax of the command is given in pdetail.doc *Note Theory and Methodology::) and it is not clear yet whether one can 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 / Rick_Venable@nih.gov