Modar commands list

  • The general syntax form of Modar commands is:

      
    command [subcommand] [keyword=<value>] [more arguments] ...

    Where the value can be an integer (int), real number (real), a string (type name, file name, a selection expression), a bool type (true or false), a vector, or a position (point coordinate) for arguments required by the command.

  Commands indexed in alphabet

 

abort

 to terminate modar with an abort signal
 

addBond

 to add covalend bond between two set atoms
 

addElectronicField

 to add an external electronic field to MD system
 

addElectronicField

 to add an external magenet field to MD system
 

addIon

 to add counter ions
 

atom

 to modify MD system in atom level
 

build

 to build MD system, topology, missing atoms
 

calc

 to calculate distance, angle, dihedral and more for current structure
 

checkMSF

 to check MD system
 

coopyCoord

 to swap coordinates
 

defgroup/defcls

 to define an atoms group
 

delete

 to delete atoms, connections ...
 

disable

 to turn off some functions
 

doEnergy

 to compute energy for current state
 

doMin

 to do an energy minimization
 

echo

 to print message
 

enable

 to turn on some functions disable by command "disable"
 

ensemble

 to specify the ensemble type, and setup thermostat and pressure control approach
 

exec

 to execute a external command
 

fourierpath

 to setup a multi-reaction coordinates path for Lambda Dyanmics
 

getVar

 to get input from user
 

goto

 to jump to a label line
 

img2box

 to move all imagable groups to the primary cell
 

imgGroup/setImgGroup

 to setup image operation group for PBC images transformation
 

include

 to load a sub Modar script file
 

lambdyn

 to setup a lambda dynamics
 

loadcrd

 to load coordinates
 

loadFFprm

 to load a force field parameter
 

loadFFtop

 to load a force field topologies
 

loadFF

 to load a force field with both topologies and parameters
 

loadMSF

 to load a Modar MSF file
 

loadMDS/loadSetup

 to load a Modar MDS file
 

loadRST/loadState

 to load a Modar RST file
 

mdcp

 to change some MD controling parameters withou rebuilding the MD core
 

nbsoft

 to enable nonbond soft cut for energy minimization due to some bad overlaping
 

nonbond

 to setup nonbonded calculation parameters
 

pbcbox

 to setup the PBC box
 

putcenter

 to declare a center group
 

quit/exit

 to quit Modar normally
 

randSeed

 to initiate the seed of random number generator
 

reactcoord/rc

 to setup a reaction coordinate
 

release

 to release memory or buffers
 

removeResidueOutsideBox

 to delete residue outside of the PBC box
 

replicate

 to build a larger system by replicating from current system
 

residue

 to mutate, patch, or insert a residue
 

resolveresidueoverlap

 to resolve residues overlapping
 

restrain

 to add restraint terms to MD system
 

rm

 to delete a file
 

runmd

 to launch MD simulation
 

savecrd/savepdb

 to save coordinates to file
 

saveFFprm

 to save force field parameters to file
 

saveFFtop

 to save force field topologies to file
 

saveMSF

 to save MD system to a Modar MSF file
 

saveMDS/saveSetup

 to save MD system setup to a compact binary file
 

saveRST/saveState

 to save MD system state to a binary file
 

segment

 to patch a segment
 

setNoseGroup

 to setup independent groups for Nose-Hoover thermostating
 

shake

 to setup constraints
 

sortTop

 to resort topology
 

steer

 to setup a steered MD
 

stopRT

 to remove rotation an translation for the atom cluster selected
 

skipEne

 to skip some energy terms
 

tell

 to restrieve various information from MD system
 

trjCalc

 to do a "calc" over a trajectory
 

trjIn

 to load trajectory files
 

trjOut

 to save trajectory from the buffer
 

trjReadNextFrame

 to load one frame from the trajectory buffer in sequence
 

trjRewind

 to rewind trajectory reading to first frame
 

verboseLevel

 to tell the verbose level
     

 

          

 

 

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  Email: support@beemd.org

 

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