A brief guide to MoDaR script language

  • Modar wraps a bounch of functions for setuping and running a MD simulation job, these functions can actually be seen as internal commands of Modar.  A simple and easy script language is implemented in Modar for concatenating these internal commands to realize all available modules designed by the developers. Taking the advantage of the script language, user can do some very flexiable modeling and complex analyzing jobs without making effort to play with the source code, developers can also save a lot of time and suffering on test stage when developing a new module.
  • Modar script language is very simlar to the Linux shell script language. Let's take a example first, bellow is the content of a script file "rst.inp" for resuming a MD simulation. 

#do a restart MD run


#     ./Modar rst.inp -o rst.log [nstepmore=100000]



#check whether variable nstepmore defined in command line

if (! -var nstepmore) {

  nstepmore=100000 #assign nstepmore a default value 100000



#load a MD system setup

loadsetup file="villin_npt.mds"


#load a restart state

loadstate file="villin_npt.rst"


#run MD for $nstepmore more steps

runmd nstepmore=$nstepmore


  To run 1000000 steps more resuming MD simulation simply by command:

 ./modar rst.inp nstepmore=1000000 –o rst_1.log 



  • The text colored in green is comment.
  • The keywords in blue are the internal commands of Modar.
  • The "if" statement is for testing whether we have a variable "nstepmore" declared, and initiate it a default value 100000 if not; As shown above, the variable "nstepmore" can be defined in command line.
  • Command "loadsetup" to load a MD sytem setup file;
  • Command "loadstate" to load a restarting state for resuming simulation;
  • Command "runmd" to launch simulation;
  • The ".mds" file is a prebuilt MD system setup and packed in binary format, it contains all data, setups and control parameters for running the MD simulation, including the restart file write out frequency and filename "villin_npt.rst" used here. So to run another 1000,000 steps more simulation just need to retype the command using the same script file but to give a new log filename for example "rst_2.log"


Here is the list of content

 Basic rules of Modar script

  1. One single line of script can only take one Modar command or statement. But one command or statement can be splited in several lines. Character “\” in the end of command line means continuous line following.
  2. Character “#” serves as a comments marker. Comments cannot be resided in the middle a sentence, only can
  3. Modar script is case insensitive except the filename used in some internal command.

 Variable and array

  • Variables in Modar scrip can be a string or a real number type, Modar can determine the type automatically according to the expression, user don’t need to declared it with a type name.
  • Modar supports one dimension array only and the member index can be negative. The array exported by Modar commands always start from 0.
  • For example:

    outputfile=”test.out”        # initiate a file name string

    istepstart=1000000           # initiate a number

    nstepmore=100000         # assign nstepmore a value 100000

    x[0]=10         # assign nstepmore a value 100000

    x[1]=20         # assign nstepmore a value 100000

    echo $istepstart                  #print the value of istepstart

    echo $x[0] $x[1]                  #print the value of istepstart

    echo $nstepmore > $outputfile     #print the value of nstepmore to file “test.out”

    where, “$” is the character for variable substitution, i.e. for getting the value of variable. Since many Modar intrinsic commands export variables (this is one of features of Modar, through those variables, user can talk with MD system), it’s better to avoid using simple variable name and to keep in mind that your variables may be overwritten by some Modar internal commands.


  • Modar supports both math expression and string expression, but they are only valid in assignment statement, if statement and while statement.
  • For example:

    #assign the sum of istepstart and nstepmore to nsteptot






  • Additionally, Modar supports selection expression in many intrinsic commands.
    For example:

    #define a atoms cluster

    defcls pocket select="segid proa && seq 26 82 99 59 56 55 46 && ! type N C O HN CA HA*"


    #to calculate the distance between a ligand and the binding pocket

    calc dist select=”pocket” select=”resname DMS

  • Math expression
    Please see here
  • Bool expression
    Please see here
  • String functions
    Please see here


 If statement

  • There are two forms of “if” statement. The short form is typed on a single line and but can specify only a single command if the expression is true.

    if ( expression ) command

    for example:

    outputfile=”test.out”    # initiate a file name string

    if(-f $outputfile) exec rm ¨Crf $outputfile


  • The long form uses else and braces to allow for blocks of commands to be nested inside the condition.

    if ( bool expression1 ) {



    else if ( bool expression2 ) {




    else {




  • For example:

    include “size.inc”             #feed a,b,c,boxl


    #get a box type from user

    getText boxtype default=”cubic” msg=”please tell the box type”


    #process the boxtype

    if($boxtype .head. "cubi") {        #cubic


      if($boxl<$b) boxl=$b

      if($boxl<$c) boxl=$c





    else if($boxtype .head. "tetr") {   #tetragonal


      if($boxl<$b) boxl=$b




    else if($boxtype .head. "octa") {   #octahidralt


      if($boxl<$b) boxl=$b

      if($boxl<$c) boxl=$c






      echo -hs "|  ** unknown boxtype: $boxtype"

      goto tellboxtype_and_abort



 While statement (loop)

  • The while statement evaluates an expression, if it is true, the shell runs the nested commands and then repeats for as long as the expression remains true. Please note that there is no short form of while statement supported, only long form as shown bellow is available.

    while ( bool expression){




  • For example:

    #load a trajectory

    trjin file="step9_harvest.trj"






      #print progress for every 10ps


      if($tmod==0) echo -hs "current MD time: $mdtime ps"


      #calculate RMSD for main chain atoms

      calc rmsd fitgroup="mainpro and name C CA N O" \

    calcgroup="mainpro and name C CA N O"

      echo "$mdtime $value" >> mainrmsd.txt


      #calculate distance between terminals

      calc dist group1="residue PROA 41" group2="residue PROA 76"

      echo "$mdtime $value" >> dist.txt


      #calculate PHI,PSI for residue 50

      calc dihe group1="atom PROA 49 C" \

    group2="atom PROA 50 N"  \

    group3="atom PROA 50 CA" \

    group4="atom PROA 50 C"


      calc dihe group1="atom PROA 50 N" \

    group2="atom PROA 50 CA" \

    group3="atom PROA 50 C" \

    group4="atom PROA 51 N"


      echo "$mdtime $PHI $PSI" >> phipsi.txt


      #calculate Radius of Gyration

      calc rgy  select="all"

      echo "$mdtime $value" >> rgy.txt





 Goto statement and label

  • Modar script supports label and goto statement, which also can serve as a loop, a switch or a psudo-routine.
  • For example:

    if(!-var boxtype) {

      echo -hs "|  ** please specify the boxtype in command line"

      echo -hs "|  for example: $scmdline boxtype=cubic"

      goto tellboxtype_and_abort


    ...   # command blocks skipeed




    echo -hs valid boxtype are:

    echo -hs "  cubic        a=b=c   alpha=beta=gamma=90 ndgf=1"

    echo -hs "  tetragonal  a=b          alpha=beta=gamma=90 ndgf=2"

    echo -hs "  rectangular a/A=b/B=c/C alpha=beta=gamma=90 ndgf=1"

    echo -hs "  orthorhombic    a,b,c       alpha=beta=gamma=90 ndgf=3"

    echo -hs "  octahidralt      a=b=c        alpha=beta=gamma=ACOS(-1/3) ndgf=1"


 Include statement

  • Modar provides include command for loading a sub-script
  • For example:

    #load force field

    include "loadff.inc"

      The contents of file “loadff.inc”:

    #load force field

    loadmtf fmt=chm file="top_all27_prot_na.rtf"

    loadprm fmt=chm file="par_all27_prot_na.prm"

    tell ff_info

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