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| 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 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 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 drude.doc* Syntax:: Syntax of the ANISOTROPY command drude.doc* Description:: Description of the ANISOTROPY command drude.doc* Toppar:: Effect on the topology and parameters drude.doc* Warnings:: To be aware of when using the ANISOTROPY command drude.doc* Examples:: Usage examples of the ANISOTROPY 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* 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 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 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-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. 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. 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 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 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 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:: PNM Command Options pnm.doc* Limitations:: Limitations of the current code pnm.doc* Examples:: Usage example pnm.doc* Installation:: How to install PNM in CHARMM environment. pnm.doc* Status:: Status of the PNM code and future development pnm.doc* References:: References for the PNM method 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 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 stringm.doc* Description:: Introduction to the string method stringm.doc* Syntax:: String method command listing stringm.doc* Function:: Description of commands and options stringm.doc* Examples:: Examples 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 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 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* 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
CHARMM Documentation / Rick_Venable@nih.gov