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Miscellaneous Commands

The commands described in this section are generally more simple in nature than those of previous sections. Some are perhaps obsolete, but included for the sake of completeness.

Syntax of miscellaneous commands

File handling:

OPEN    UNIT integer NAME filename [WRITe ]   [UNFORMatted]
                                   [READ  ]   [FILE]
                                   [APPEnd]   [FORMatted]
                                              [CARD]

LOWEr                                 ! Force the case of output file names
UPPEr                                 !             "

CLOSe   UNIT integer  [DISPosition KEEP  ]
                      [DISPosition DELEte]

REWInd  UNIT integer

REWFalse ! do not allow rewinds during trajectory I/O
REWTrue  ! allow rewinds during trajectory I/O

INQUire ! get a list of open files and their qualifiers, only from CHARMM
        ! possible

STREam  [ UNIT integer       ] [ repeat(argument) ]
        [ file_specification ]        ! Call another input file


OUTUnit  integer                      ! Redirect output to a different unit.

RETUrn                                ! Return to the previous unit

DEFIne  keyname  SELE atom_selection END

SYSTem  "shell-cmd"  ! Execute a shell command (Unix)

STOP               ! Terminate CHARMM

USER ....          ! Invoke a user supplied subroutine (USERSB)

PREF               ! Print out pref.dat keywords that were used during
                   !     compilation of running executable

[ECHU [integer]]   ! Print remainder of commandline to OUTU or to file open on
ECHO ....          ! the unit specified with ECHU integer. Just ECHU resets
                   ! echo-unit to OUTU.

Title manipulation:

TITLe  [COPY]           ! Specify the main "write" title

WRITe TITLe [UNIT int]  ! output a title to the specified unit without
                        ! closing the file and without initial "*"s.
                        ! ***** (only from main command parser)

Control levels:

TIME  {integer}      ! Specify the timing level for performance evaluation
      {NOW    }      ! Show current time.
      {DIFF   }      ! Show elapsed time since last timed event

DATE                 ! Display the current date and time

WRNLev int [NODE int]! Set the warning print level. Higher values mean
                     ! more warnings printed (default: 5).
                     ! If running in parallel, only node 0 is modified
                     ! unless another node is specified.

PRNLev int [NODE int]! Set the print level. Higher values mean
                     ! more printout (default: 5) (default: all nodes).

IOLEv int [NODE int] ! Set the I/O level (not for normal use)

BOMBlev integer      ! Set the error termination level
NOBOmb               ! Don't bomb on typing errors (same as BOMBlev -1).

FASTer  [integer]    ! Specify efficiency level
        [OFF    ]    ! Disable fast routines
        [DEFAult]    ! Use fast routines if possible.
        [ON     ]    ! Use fast routines, otherwise error.
        [SCALar ]    ! Use scalar fast routines.
        [VECTor ]    ! Use vector fast routines.
        [VPAR   ]    ! Use vector/parallel fast routines.
        [CRAYvec]    ! Use vectorized CRAY fast routines.

LONG                 ! specify long line output (<256 characters)
SHORT                ! specify short line output (<80 characters)

Quick and simple structure analysis:

QUICK { repeat(atom-spec [COMP] ) } ! one atom     - position and projection
Q                                   ! two atoms    - distance
                                    ! three atoms  - angle
                                    ! four atoms   - dihedral
                                    ! five or more - list positions only

      atom-spec::= { residue-number atom-name  }
                   { segid  resid atom-name    }
                   { BYNUm  atom-number        }
                   { atom-selection [MASS]     }
                   { atom-number ***           }

If only one atom is specified its position will be printed as well as its relationship to the previously defined axis (if any). (e.g. COOR AXIS command).

If the keyword “COMP” immediately follows an atom specification (or atom selection), then the comparison coordinate value(s) will be used for that atom only.

If atom selections involving multiple atoms are specified, the center of geometry or center of mass of each atom selection will be used as the coordinate for the analysis. Note that if mass weighting is used, the keyword MASS must immediately follow the associated atom selection.

Note

This is the old syntax. It may be used only if ALL atoms are specified in this manner (simple integers) and no COMP feature is allowed.

The QUICK command sets the following substitution paramters (for use subsequent commands);

one   atom  specified - @XVAL, @YVAL, @ZVAL
two   atoms specified - @DIST
three atoms specified - @THET
four  atoms specified - @PHI

Some examples:

--- bond distance using atom selections ------------
       quick sele atom aseg 53 HN end sele atom aseg 53 N end
--- Angle using atom selections ------------
       quick sele atom aseg 53 HN end -
             sele atom aseg 53 N end  -
             sele atom aseg 53 CA  end
--- Dihedral using atom selections ------------
       quick sele segi buta .and. type C4 end  -
             sele segi buta .and. type C3 end -
             sele segi buta .and. type C2 end -
             sele segi buta .and. type C1 end
--- Dihedral using segid/resid/atom ------------
       quick buta 1 C4  buta 1 C3 buta 1 C2 buta 1 C1 end
--- Using simple atom numbers -----
       q 1 2 4   ! bond angle involing atoms 1-2-4
       q 1 2 4 6 ! dihedral involving atoms 1-2-4-6
--- Using a mixture of formats -----
       q 1 CL 2 N sele ires 4 end MASS B 1 C COMP
          ! dihedral involving atoms:
          ! ires 1 CL -- ires 2 N -- center of mass of ires 4 --
          ! and the comparison coordinate value of atom B 1 C.
--- distance between center of mass of two segments-----
       quick sele segid A end MASS sele segid B end MASS
--- distance between an atom and its comparison coordinate value-----
       quick sele atom aseg 53 HN end sele atom aseg 53 HN end COMP

RANDom and IRANdom specifications:

RANDom  OLDRandom
        CLCG
        UNIForm         [SCALe scale]  [OFFSet offset]  [ASIN]   [ISEEd  iseed]
        GAUSsian sigma                                  [ACOS]

IRANdom                 [SERIes int]  [SETUp]  [BEGInt int]  [ENDInt int]
                        [SEED int]

Run control:

Command line sustitutions:

SET parameter string                      ! Define a parameter

CALC parameter arithmetic_expression      ! Evaluate an arithmetic expression

command  ........ @parameter ........     ! use a parameter in a command
command  ........ @?parameter ........    ! existance of parameter

command  ........ ?energy-term ........   ! use an energy value in a command

command  ........ ?corman-value ........  ! use a corman value in a command

SHOW [BUILtins]                           ! list all "?" substitution values.
SHOW PARAmeters [VERBose]                 ! list contents of parameter table

IF [parameter] [ EQ ] [ string] [THEN] command ! process a conditional
   [string** ] [ NE ]                     ! (**= single character not allowed
               [.EQ.]                        unless from @ or ? variables)
               [.NE.]
                                          !
IF [parameter] [ GT ] [ value ] [THEN] command ! process a conditional
   [value**  ] [ LT ]                     ! (**= single character not allowed
               [ GE ]                        unless from @ or ? variables)
               [ LE ]
               [ AE ]                     ! AE = almost equal (diff<0.0001)
               [.GT.]
               [.LT.]
               [.GE.]
               [.LE.]
               [.AE.]
The following forms are also allowed, and may be nested
IF ... THEN
statements
ENDIF

IF ... THEN
statements
ELSE
statements
ENDIF

GOTO label                                ! A branching command

LABEL label                               ! Label (up to 20 characters)
                                            that may be branched to

INCRement  parameter [ BY value ]         ! Do an addition

DECRement  parameter [ BY value ]         ! Do a subtraction

GET        parameter UNIT int             ! read a parameter string

FORMat  [ (format_spec) ]                 ! Specify a format for encoding.

TRIM  parameter [ FROM integer ] [ TO integer ]  ! Take a substring

MMQM [atom-selection] [UNIT integer] [NCHAr integer]
                                     ! Write selected QM atoms together
GAUSSIAN_HEADER                      ! with the rest of atoms as charges
<gaussian commands>                  ! as input to GAUSSIAN program
END
GAUSSIAN_BASIS
<optional gaussian general basis set specification or other input>
END

NCHAr specifies the number of characters of the atom type that will be output. The default is one (NCHAr=1) such that, for example, for that atom type HG1, only the character H will be printed in the output file.

If CHARMM is compiled with Q-Chem then MMQM is slightly modified to function as a Q-Chem input writer instead of Gaussian. The modified routine should be called in the following way.

MMQM [atom-selection] [UNIT integer]
$rem section
$molecule section but do not $end it
QCHEM_MOLECULE
$end for $molecule section
QCHEM_MISC
add any additional Q-Chem input sections
END

  • DEADline commands:

    DEADline [CPU real] [CLOCk real]                 ! Time limits for job
    
    [SYNTAX ATLImit]
    
    ATLIimit alternate_command                       ! Execute if limits reached

For assignment:
parameter::= string containing alphanumeric or non-alphanumeric characters
(no white-space (blanks or tabs)
For substitution:
parameter::= string-containing- alphanumeric-characters
parameter::= {string containing lphanumeric or non-alphanumeric characters}

energy-term::= see *note eterm:(chmdoc/energy.doc)Skipe.

  • Convex ONLY:
SPECIfy  specify-keywords

  specify-keywords ::=
                      PARAllel [NCPU integer-number-of-cpus] |
                      FLUSh |
                      NOFLush |
                      NBFActor  real-nonbond-memory-factor |
                      FNBL { ON | OFF }

Purpose of the various miscellaneous commands

  1. The OPEN command is used to open logical units to specific files specified from the input file rather than logical name assignments made prior to the run. This is the recommended procedure to access a file within the program. OPEN can be used to redirect the output that appears on unit 6 to different files by opening unit 6 in the middle of a run. The APPEnd keyword causes output to be appended to the output file; useful if you want to get back to your normal output file without sacrificing the first part of it.

    The case of filenames opened for WRITE access may be specified with the LOWEr or UPPEr commands.

  2. The CLOSe command closes a logical unit. This frees the associated file and logical unit so that they can be used for other purposes. The default disposition of the file is KEEP.

  3. The REWInd command

    The REWInd command causes the requested logical unit to be rewound. When used with the STREam command, a particular sequence can be used more than once.

  4. The STREam command

    The steam command allows the input of command sequence to be shifted to another file. This is useful when parts of an input file are to be used many times or used by many different calculations. The only input value is the unit number to transfer to. In place of a unit number, a file may be specified. Stream files must be card format and should begin with a title.

    Arguments may be set by the stream command. Arguments must not contain any blanks (or other delimiting characters). They are assigned to the variable IN1, :/RAIN2, IN3, etc.. The command;

    STREam filename  arg1  arg2  arg3  arg4

    is functionally equivalent to;

    SET IN1 arg1
    SET IN2 arg2
    SET IN3 arg3
    SET IN4 arg4
    STREam filename

    This simplifies the use of passed parameters to a stream file.

  5. The RETUrn command

    The return command causes the input of command sequence to return to the stream that called the current stream. Streams may be nested to up to 20 calls. There are no parameters for this command

  6. The DEFIne command

    This command allows the user to specify selection keywords. This command must contain a keyword and an atom selection. The keyword may then be used in subsequent atom selections. The keywords may not be abbreviated.

  7. The SYSTem command

    Allows shell commands (sh, csh, ksh, etc.) to be executed from within CHARMM. NOTE: CHARMM assumes all shell commands are protected by double quotes, e.g., system “awk -f file.awk p1=1 p2=3 filename > filout” will process the file filename using the awk script file.awk and the parameters p1=1, p2=3 placing output in file fileout.

  8. The STOP command

    The STOP command causes the program to terminate and to ignore all command that follow this command. This is useful for making temporary modifications to input files.

    Note

    This command is only available from the main program.

  9. The USER command, see Interface.

  10. The PREF command will prting out the pref.dat keywords that were used in the current executable. The purpose is to allow the user to probe the executable about whether the feature(s) that are desired were in fact compiled into the executable and whether one can expect certain features to work. Currently these are the keywords that will be checked for and printed. If keywords other than the following were used, they will not be detected or printed.

    ACE ADUMB AIX370 ALLIANT ALPHA ALPHAMP AMBER APOLLO ARDENT
    ASPENER BANBA BLOCK BUFFERED CADPAC CFF CHARMMRATE CM5 CMPI
    COMMEASURE CONCURR CONVEX CRAY CRAYVEC CRAY_1DFFT CSPP
    DEBUG DEBUGGB DELTA DIMB DMCONS DOCK EISPACK ETHER
    FILEINPUT FILEOUTPUT FMA FOURD FSSHK GAMESS GBBLCK GBFIXAT
    GBINLINE GBNOLIST GBSWIT GENBORN GENCOMM GENETIC GLDISPLAY
    GNU GRAPE GWS HMCM HPUX IBM IBMRS IBMSP IBMVM IMCUBES INTEL
    IPRESS IRIS JUNK LARGE LATTICE LDLAN LDM LDMGEN LMC
    LONEPAIR LONGLINE LRST MANYNODES MBOND MC MCSS MMFF MOLVIB
    MPI MTS MULTCAN NEWTIMER NIH NOCORREL NODISPLAY NOGRAPHICS
    NOIMAGES NOLDMUP NOMISC NOPARASWAP NOST2 NOVIBRAN NO_BYCC
    NO_BYCU NO_DQS OLDDYN OS2 OTHERPARSHK PARAFULL PARALLEL
    PARALLELSHK PARASCAL PARVECT PATHINT PBC PBCUBES PBEQ
    PBEWALD PBOUND PERT PM1 PMEPLSMA PNOE POINTER_KEYWORD POLAR
    POSIX PREFMSI PRIMSH PVM PVMC QBLOCK QUANTA QUANTUM REDUCE
    REPDEB REPLICA RGYCONS RISM RXNCOR SAVEFCM SCALAR SCHED
    SGIMP SGMD SHAPES SHMEM SINGLE SOCKET SOFTVDW T3D T3E TERRA
    TIMESTAMP TNPACK TRAVEL TSM UNICOS UNIX UNUSED VAX VECTOR
    XDISPLAY XLARGE XSMALL YAMMP

    See also Command Line Substitution Parameters for variable substitutions for detecting the keywords.

  11. The TITle command is used to modify TITLEA which is used whenever a file is written. This title is normally filled only in the CHARMM startup procedure. If the COPY keyword is used, then the TITLEB (the title from the most recently read file) is copied to TITLEA. Otherwise, a valid title specification should follow this command.

  12. The TIMEr command sets the value of TIMER in COMMON /TIMER/ to the specified value. This variable is used to time different functions in the program.

    • 1 will print out the time to evaluate ENERGY.
    • 2 will print out individual component times in ENERGY, and the times for various components of the EXEL nbonds update.
  13. The WRNLEV command sets the value of the WRNLEV variable in COMMON /TIMER/ to the specified value. This is used in WRNDIE and elsewhere. Suggested values for future use:

    -5,5

    warnings associated with fatal errors (see BOMBlev).

    5

    default should print brief warning and error messages for conditions that will affect outcome.

    6

    more extensive information on errors and some information on normal partial results and conditions

    7

    verbose error messages and more normal processing information for debugging

    8

    all information that might be relevent to an error condition plus checking results

    9,10

    debugging levels for anything you might concievably want.

    10 or higher

    for term by term outputs from energy routines, or other tasks where huge amounts of data useful only in debugging might be generated.

  14. The BOMBlev command sets the level which determines the types of errors which will terminate the program. The default is zero. A value of -1 is suggested for interactive use. Suggested values are;

    -5,-4

    Limit exceeded type of errors. Run only as debug.

    -3,-2

    Severe errors where results will be incorrect if continued.

    -1

    Moderately severe errors, results may be bad.

    0

    Parsing type errors. Some important warnings.

    1,2

    Serious warnings.

    3,4,5

    Assorted minor warnings (see WARNlev for their suppression).

  15. The FASTer command controls when and whic fast energy routines will be used.

    Certain conditions must be met in order to use the fast routines. If the fast routines are requested and cannot be used, an error message will be issued and the slow routines will be substituted. Also, there is less error checking for the fast routines. See fast.

  16. The SET command sets up a command line parameter. The command line parameters will be substituted into the command line by the command line reader when it encounters the symbol “@”.

    A command line parameter token can now be a string rather than just one of the single characters 0-9,a-z,A-Z. For substitution a token is indicated by the use of the @ character as before. Arrays can be made by preceding the array indices with ‘@@’, e.g. @segid@@j can be used to loop over parameter tokens segid1, segid2, ... (Note: Pete Steinbach’s precursor to PARSUB, called to first substitute parameters preceded by ‘@@’. Allows parameters to reference array elements. Mar 20, 1998)

    The token is end-delimited by any non-alphanumeric character. In the case that the token is not found in the parameter table, a check is made to see if the first character of the token is itself a token in the parameter table. If this single character token is in the table, the corresponding value is substituted – this is the necessary scheme to allow backwards compatibility with the old parameter substitution, which allowed parameters embedded in strings. For unambiguous token detection, “protect” the token with brackets {} — this allows for the use of non alphanumerics in tokens such as -,_. To test whether a token is in the parameter table, use @?token. This will substitute 1 if token is in the table, 0 if not. This is useful (in conjunction with the IF command) for setting defaults. (Note that @? takes precedence over any of the built-in parameters such as ?ENER etc. — it is parsed first).

    SET outfile = myjob
    OPEN UNIT 1 WRITE CARD NAME @outfile.dat

    In the above example the token is delimited by the ”.” in the filename and the value “myjob” is substituted in place of “@outfile”, resulting in an unit 1 being attached to the file “myjob.dat”. To protect a token from surrounding alphanumerics, use brackets,

    OPEN UNIT 1 WRITE CARD NAME @{outfile}today.dat
    File name becomes "myjobtoday.dat".

    The token is taken to be whatever is delimited by the brackets — thus the token may in this case may also contain non-alphanumerics.

    SET max-temp = 500.
    DYNA VERLET FINALT = @{max-temp} ... etc...

    For backwards compatibility, get token, check in table, if not present, then drop back to first character of token and check again. Substitute appropriately.

    SET 1 rdie
    OPEN UNIT 1 WRITE CARD NAME @15.dat

    will result in a file named rdie5.dat

    To test the presence of a token in the parameter table use the @? operator. If the token is present, the value substituted is 1, if not 0. This is useful for setting defaults:

    if @?{max-temp} .eq. 0 set max-temp 300.

    At present the parameter table is dimensioned as follows:

    Maximum number of parameters

    256

    Maximum token length

    32

    Maximum value length

    128

    For current sizes use command SHOW PARAmeters VERBose (see below).

  17. The SHOW command prints the available command line substitution parameters.

    SHOW by itself or with BUILtin keyword prints the parameters set internally by the program functions, such as ?ENER, ?RMS etc. SHOW PARAmeters lists the user defined @ command substitution parameter table. The VERBose keyword prints table limits on string sizes for tokens and values.

  18. The IF command will optionally execute a command based on the value of the parameter used. Example;

    IF 1 GT 25.0  PRINT COOR

    The “EQ” and “NE” operations only compare strings. Thus the string “2.00” would not be equal to “2.0” with these conditions. The options requesting a value, do a value comparison. The AE option will test if two values are almost equal (difference less than 0.0001). This avoids the problem of round off error in loop counters (i.e. values like 3.999999).

  19. The GOTO command will rewind the current input stream and search for the requested label. For the sake of efficiency, frequent use of this command (i.e. looping) should not be used with long input files.

  20. The LABEL command does nothing except mark the presence of a label (up to 20 characters in length) to be used by the GOTO command.

  21. The INCRement command will modify the selected parameter. If a value is not specified, then a value of 1.0 will be used. Example

    INCR 1 BY 2.0
  22. The DECRement command is identical to the INCRement command except that a subtraction is done. The purpose of this command is to allow the subtraction of parameters. For example, the sequence;

    SET 1 ?ENER
    DECR 1 BY ?HARM
    WRITE TITLE UNIT 30
    * @1
    *

    will compute the total energy less the constraint energy and write it to a file.

  23. The FORMat command allows the user to specify the format for ALL subsequent calls to ENCODF. This can be used to format the output of titles or other internal strings. Here are some examples;

    FORMat (I5)

    All values will be integers. Good for looping and such.

    FORMat (F12.4)

    Just what it says.

    FORMat

    Reverts to current scheme for ENCODF (1PG14.6) followed by trimmimg

    FORMat (A12)

    Won’t work...

    If an integer format is used, the real value will be rounded to the nearest integer. The parenthesis are required around the format specified. If several different formats are needed, then the FORMat command should precede each different required usage.

    Note

    Not all string manipulation commands call ENCODF. The SET command does not. The INCRement command does, so the sequence;

    FORMat   (f10.5)     ! specify the format
    INCRement  a  by 0.0 ! apply the format to variable "a"

    may be used to format a particular variable without modifying its value.

  24. The TRIM command allows a substring of a parameter to replace the same parameter. The FROM value determines the first character to be kept (default first nonblank character), and the TO value determines the last character to be kept (last nonblank character). If a TO value that is larger than the length of the current parameter is used, blanks will be padded at the end.

    Preceding blanks may be added by;

    SET 5           ! set parameter five to the null string
    TRIM 5 to 10    ! convert parameter five to a string with 10 blanks
    SET 6 @5@6      ! add these 10 blanks to parameter six

    This command may be used for general formatting.

  25. The DEADline command sets CPU and/or clock-time limits. These limits are checked in DCNTRL,ECNTRL, and GAUSHS (the parameter-fitting routine) at regular intervals. When a deadline has been reached the routine exits normally. This is useful when you have to stop computing before a given time of day (taking advantage of lower charge during the night or some such) or when you want to get some useful results and you are not sure that you can actually stay within the CPUlimit in a given batch queue.

    Keyword CPU <real> specifies that <real> CPUminutes from the time the command is given is to be one deadline.

    Keyword CLOCk <real> sets the time HH.MM (in 24-hour format) as one deadline. The routine assumes that if the command is issued after the specified time, you mean the following day. (If at 6 pm you start a job containing the line DEAD CLOC 13.00 CPU 600. your minimization will run until 600 CPU-minutes have been used, or until 1 pm the next day, whichever comes first.)

  26. The ATLImit command can be given at any point in the input file. CHARMM checks before reading each command if either of the DEADlines (CPU or CLOCk) has been reached. If this is the case the alternate_command of the most recent ATLImit command is executed. This would typically be a GOTO SHUTdown or some other simple thing, but could be any CHARMM command. Currently the alternate_command is limited to 80 characters.

  27. Substitutions and punctuation in command input.

    ”!”

    Ignore this and all subsequent characters on this line

    “-“

    If this is the last character of a line then the following line is a continuation

    “*”

    As a first character indicates a title line. Alone on a line indicates a title terminator.

    “$”

    The default delimiter

    “* % # +”

    Atom selection wildcards, alone or in a word

    *

    matches any string of characters (including none),

    %

    matches any single character,

    #

    matches any string of digits (including none),

    +

    matches any single digit.

    “@”

    Command parameter substitution

    ”?”

    Energy value substitution


  1. File inquiry. The inquiry command (from CHARMM) may be used to get a list of currently open files. This is very useful in interactive sessions when one has forgotten which FORTRAN units are already assigned. The command won’t work if the files are assigned outside of CHARMM.

  2. Random number generation.

    1. RANDom command. The expression ?RAND will have a random number substituted for it during command line evaluation. The default is to provide a number from a uniform distribution, between 0.0 and 1.0; the RANDom command allows modification of the distribution type and specification of other factors. The only required keyword is the distribution type, which must be second; for a GAUSsian distribution, a value for sigma is required; the default mean is 0.0.

      RANDom  OLDRandom
      CLCG
      UNIForm         [SCALe scale]  [OFFSet offset]  [ASIN]   [ISEEd  iseed]
      GAUSsian sigma                                  [ACOS]

      Additional keywords:

      SCALe scale

      multiply the number by scale

      OFFSet offset

      add offset to the number

      ACOS

      treat the number as a cosine and return the angle (deg)

      ASIN

      treat the number as a sine and return the angle (deg)

      ISEEd iseed

      specify a new random seed (integer)

      Examples:

      RANDOM GAUSS 0.2 SCALE 10.0   !     gaussian  mean of 0.0 with a sigma of 2.
      RANDOM UNIFORM SCALE 360.     !     uniform   0. to 360
      RANDOM UNIFORM ACOS SCALE .5  !     uniform   angles with cosines from 0. to .5
      RAND GAUS 5. OFFS 60.         !     gaussian  mean of 60. with a sigma of 5.
      RAND UNIF ISEED 7734          !     uniform   new random seed

    Subsequent use of ?RAND will substitute a number from the appropriate distribution.

    Note that OLDRandom subcommand sets OLDRNG, which runs “old” random number generator instead of “new” CLCG method. CLCG unsets OLDRNG, and runs the CLCG random number generator.

  1. IRANdom command. This command is designed to generate series of random integers taken from uniform distributions between user-specified limits. Each series or distribution must first be set up with the IRANdom SETUp command, in which the lower and upper limits of the distribution, the series number, and an integer seed are specified. E.g.

    IRAND SERIES 1 SETUp BEGI 1 ENDI 18  SEED 2346
    IRAND SERIES 2 SETUp BEGI 1 ENDI 402 SEED 4028987

    The random integers for each series are then generated with the commands

    IRAND SERIES 1
    IRAND SERIES 2

    The ?iran expression accesses the last random integer generated.

    The purpose of the multiple series feature is at least two-fold. First, it allows users to generate random numbers easily from many different distributions during the same CHARMM run (e.g. for use in different parts of the same calculation). Second, it may help the user avoid correlations between random numbers generated for different parts of a calculation. An internal counter, corresponding initially to the seed, is incremented by several units with each instance of the IRANdom command; by separating the seeds of the various distributions sufficiently, the user can thus avoid cross-series correlations. The use of multiple seeds for a given series should be unnecessary and is discouraged. The IRANdom function has an overall period of no less than 10^12 for distribution widths of 10^10 or less. IRANdom can also be used to effectively generate random real numbers, through a division of the generated integers by a constant, with the use of the CALC command.


  1. The CALC command allows the evaluation of any fortran-admissible arithmetic expression. It supports most of the normal fortran functions such as COS, SIN, TAN, EXP, LN, LOG, TANH, etc... Any number of parenthesis nesting is allowed. The substitution parameters @ is allowed directly. The substitution parameters ? can also be used but the character chain must be surrounded by blanks to be properly recognized; e.g., COS( ?pi ) is ok but not COS(?pi). Otherwise, there can be any number of blanks between the quantities involved in the arithmetic expression. See the testcase calc.inp for examples.

    Note

    All transcedental functions work in natural units (not degrees).


  1. Writing input for GAUSSIAN series of programs. Selected atoms are treated as quantum atoms while the rest of the system is put at the end of the file in a format ready for CHARGE command within GAUSSIAN (must be at least version 92) Gaussian commands are specified after GAUSSIAN_HEADER keyword ended by the END keyword, and other input is optionally specified after GAUSSIAN_BASIS keyword. If none of the two is specified both END keywords must still be present. There is no check for the names of atoms not specified according to periodic table of elements. Use RENAme ATOM command to rename CA atoms for example. Charges are taken from RTF.

    MMQM [atom-selection] [UNIT integer]
    GAUSSIAN_HEADER
    # 6-31g** charge scf=direct mp2=fulldirect gen
    END
    GAUSSIAN_BASIS
    <optional gaussian general basis set specification or other input>
    END
  1. Example using MMQM to write Q-Chem input file:

    MMQM [atom-selection] [UNIT integer]
    $rem
    .... add all rem variables ....
    $end
    
    $molecule
    0 1
    QCHEM_MOLECULE
    $end
    
    QCHEM_MISC
    .... add additional Q-Chem input sections ....
    this is the place to specify an $opt section and add
    constraints for performin entire PES scans
    END

  1. SPECIfy specify-keywords ! Convex ONLY

    specify-keywords ::=
                         PARAllel [NCPU integer-number-of-cpus] |
                         FLUSh |
                         NOFLush |
                         NBFActor  real-nonbond-memory-factor |
                         FNBL { ON | OFF }

    description:

    1. PARAllel - Tells CHARMm to run parallel (where possible). The optional NCPU keyword specifies the maximum number of processors to use. If a number is specified that is greater than the maximum allowed for the particular machine, a warning message is printed and the number of cpu’s is set to the maximum. Note that at startup CHARMm senses the number of cpu’s and sets NCPU accordingly.
    2. FLUSh - Specifies the that trajectory; coordinate; dynamics restart and other output files should be flushed after each data set is written. See below. This is the default action. The command is provided to reset
    3. NBFActor - When the parallel non-bond list generators allocate memory for the temporary arrays used by each thread, the predicted size of list array (MXJNB and the like), is divided by the number of cpu’s and multiplied by NBFACT. The default is 1.5 and has worked well so far. If it doesn’t the SPECIfy NBFACT <num> command is available to adjust it.
    4. FNBL - FastNonBondListgeneration - Specifies whether or not to use the new non-bond list generation routines. Just included for testing and timing purposes.

  1. IOFOrmat [ EXTEned | NOEXtended ]

    In c30a2, atom numbers can assoume I10 and PSF IDs (SEGID, RESID, RES and TYPE) can be character*8. Atom numbers take I5 in coordinate files and I8 in psf files and CHARACTER*4 PSF IDs are used for Normal (noextended) I/O operation. These are expanded to I10 and A8 respectively. Noextended format is the default and the expanded format is used only when the number of atoms is greater than 100000 or any PSF ID is longer than 4 characters. This command overrides the default set: IOFOrmat EXTEnded enforces the extended format and IOFOrmat NOEXtended does the normal (old) format.