CHARMM Element doc/usage.doc 1.1#File: Usage, Node: Top, Up: (chmdoc/charmm.doc), previous: (chmdoc/install.doc),Next: (chmdoc/support.doc) How to use CHARMM The user of CHARMM controls its execution by executing commandssequentially from a command file or interactivly. In general the orderingof commands is limited only by the data required by the command.For example, the energy cannot be calculated unless the arrays holdingthe coordinates, the parameters, etc., have already been filled. This section deals with overall usage, as opposed to thedetailed description of any given command. This is a good place tostart when first learning CHARMM.* Menu:* Meta-Syntax:: Describing the Syntax of Commands* Command Syntax:: Rules for composing command input files.* Run Control:: Ways to modify control flow and stream switching.* I/O Units:: Correspondence between files and unit numbers used by CHARMM.* AKMA:: Units of Measurement used in CHARMM* Data Structures:: Data Structures used by CHARMM* Standard Files:: Descriptions of parameters, topologies, and coordinates available.* Examples:: Sample runs* Interface:: How to make your own private version of CHARMM* Syntactic Glossary:: Glossary of syntactic terms* Glossary:: Glossary of non-syntactic terms.#File: Usage, Node: Meta-Syntax, Up: Top, Next: Command Syntax, Previous: Top Rules for Describing the Syntax (The Meta-Syntax) The syntax of commands is described using the following rules:Capitalized words are keywords that must be specified as is. However, ifthe word is partially capitalized, it may be abbreviated to thecapitalized part. Lower case words are to be replaced by a correspondingdata entry. The symbol "::=" means "has the following syntactic form:".Anything enclosed in square brackets, "[]", is optional. If severalthings are stacked in square brackets, one may choose one optionally.Anything enclosed in curly brackets, "{}", specifies that a selectionmust be made of the choices stacked vertically inside. The syntacticentities which appear as an argument to "repeat" may be repeated anynumber (including zero) times. Defaults for optional parameters may beenclosed in apostrophes and placed under the entity they stand for.However, defaults are not specified in this manner if the rules for thedefault are complex. The syntactic glossary, see *note glossary: Syntactic Glossary,contains further syntactic entities which are used in the commanddescriptions. Finally, the options and operands in each command canusually be specified in any order except if otherwise noted.#File: Usage, Node: Command Syntax, Up: Top, Next: Run Control, Previous: Meta-Syntax Command language rules and loreA CHARMM run is controlled by a command file (or files).This section of the documentation describes the basic rules forthe command file. Details of command level run control are describedin the next node. A command file for CHARMM should begin with a specification ofthe title of the run. (See the syntactic glossary, *note syn: syntacticglossary, for the syntax of a title.) Then, any number of commands maybe specified. Each command consists of a command line possibly followed byother data. The command line is scanned free field. This command linemay be longer than one line in the file; to do this, one must place ahyphen at the end of line which is to be continued on the next line.Comments may be placed on a command line by preceding the comments byexclamation points. All lower case characters are converted to uppercase. This format is identical to that used by the VAX command languageinterpreter. In addition, blank lines are permitted to separate blocksof commands for increased readability. The first word of every command line specifies the command.Generally, required operands of a command must follow in order.On the other hand, options may generally be specified in anyorder. Further, any number is always preceded by a key word so that anynumeric operands, can be placed in arbitrary order. The command line is scanned in units of words and delimitedstrings. A word is defined by a sequence of non-blank characters, Adelimited string consists of a keyword followed by a string ofcharacters of variable length followed by a delimiter string.One example of where a delimeter string is used is in atom selectionwhere the syntax is; SELE ...... END. Note, that the "END" is required anddelimits the atom selection. Abbreviations are permitted in various contexts. The first wordmay be abbreviated to four characters and numerous options and operandsmay also be abbreviated to four characters. However, some key words whichare used to mark numbers may not be abbreviated. See the processing forindividual commands to see what can and cannot be abbreviated. Many of the various options and numeric values are maintainedfrom one invocation of a command to the next. Once a value is specified,it is maintained until it is changed in any command. Therefore, if CUTNBis specified in a NBON command, that value will be used in the DYNAcommand unless it is changed therein. Usually, when a free field command line is read in, it isechoed onto a standard output. Each such echo will be prepended by a shortmarker, eg. "CHARMM>", which identifies the line of input as well as thecommand processor which is interpreting it. In general, as each of the command is interpreted, it is deletedfrom the command line. When command processing is finished, a check ismade to see that nothing is left over. The presence of extraneous junkindicates that something was mistyped. For some commands, such as DYNAmics,where a mistake may be costly, extraneous characters result in a fatalerror.#File: Usage, Node: Run Control, Up: Top, Next: I/O Units, Previous: Command Syntax Controlling a CHARMM RunIF command-parameter test-spec comparison-string command-spec GOTO label-string LABEL label-string STREAM [UNIT integer] [file-specification] RETURN SET command-parameter string INCRement command-parameter [BY real] DECRement command-parameter [BY real] This node describes commands that are used to modify the usualsequential interpretation of commands from the command file.