Modar internal command:

 tell

To retrieve various information, such as system summary of MD system, summary of force field, number of segments for a selection, number of residue of for a selection, number of atoms for a selection ...

  • Syntax
     
    tell <subcommand> [arguments] ...

  • Subcommands and examples
    • nseg

      #to tell segments count in the system

      tell nseg   select="ALL"

        Variables exported

      nseg

      Number of segments in selection


    • nres

      #to tell residues count in “segn PROA”

      tell nres   select="segn PROA"

        Variables exported

      nres

      Number of residues in selection


    • natom

      #to tell atoms count in the “residue PROA 2”

      tell natom   select="residue PROA 2"

        Variables exported

      natom

      Number of atoms in selection


    • seg/segment

      #to tell the info. about first (0th) segment in the system

      tell seg id=0 select="ALL" 

      tell seg  0 select="ALL"  #keyword id can be omitted

        Variables exported

      segn

      The segment name querried

      nres

      Residue counts in the segment querried

      natom

      Number of atoms in the segment querried

      segtype

      The type of segment queried (known types: protein, dna, rna)


    • res/residue

      #to tell the info. about first residue in “segn PROA”

      tell residue id=0  select="segn PROA"

       

      #to tell the info. About second residue in “segn PROA”

      tell residue 1  select="segn PROA" #keyword id omitted here

      The residue index starts from 0. If the “id” given is larger than the total number of residues selected, the last residue will be reported. i.e. if “segn PROA” has 100 residues, following commands both report the information of last residue.

      tell residue 99   select="segn PROA"

      tell residue 100  select="segn PROA"

        Variables exported

      resn

      Name of residue queried

      iseq

      Sequence index of residue queried

      Segn

      The segment name of the residue belonging

      natom

      Atom count of residue queried


    • resn
      It is similar to subcommand “res”, but only exports variable “resn”


    • farRes

      #to tell far water to origin

      tell farres center=(0,0,0)  select="resn tip*"

        Variables exported

      ResExpr

      Residue expression, which can be used in select expression directly


    • farOutBoxRes

      #to tell far water outside box

      tell faroutboxres select="resn tip*"

        Variables exported

      ResExpr

      Residue expression, which can be used in select expression directly


    • closeRes

      #to tell close water to origin, the mass center used for evalation

      tell closeres center=(0,0,0)  select="resn tip*" mcenter=true

        Variables exported

      ResExpr

      Residue expression, which can be used in select expression directly


    • seq
      It is similar to subcommand “res”, but only exports variable “seq”


    • atom

      #to tell the info. about third atom in ¡°residue PROA 1¡±

      tell atom id=2  select="residue PROA 11"

      tell atom 2  select="residue PROA 11" #keyword id can be omitted

        Variables exported

      atname

      the atom name queried

      atx

      coordinate X value of atom queried

      aty

      coordinate Y value of atom queried

      atz

      coordinate Z value of atom queried

      atmass

      Mass of atom queried

      atcharge

      Charge of atom queried

      atgamma

      Langevin friction coefficient of atom queried

      atvdwr

      VdW radius of atom queried

      attype

      Force field type name of atom queried


    • atomn

      It is similar to subcommand “atom”, but only export variable “atomn”.


    • atomcrd
      It is similar to subcommand “atom”, but only export coordinates relevant variables “atx”, ”aty”, ”atz”


    • atommass

      It is similar to subcommand “atom”, but only export variable “atmass”


    • anglewithplanexy

      tell anglewithplanexy group1="group 1" group2="group 2"
      to tell the angle with horizontal plane


    • anglewithaxisz

      tell anglewithaxisz group1="group 1" group2="group 2"

      to tell the angle with Z axis


    • hydrogenbond

      tell hydrogenbond accepters="residue PROA 1" donors="resn TIP*" len=2.5 th1=105 th2=105

      to tell the hydrogenbond between accepters and donors sepcified



    • mass/totmass

      #to tell total mass for “segn PROA”

      tell totmass  select="segn PROA"

        Variables exported

      totmass

      Total mass of selection


    • charge/totcharge

      #to tell the total charge of system

      tell charge  select="ALL"

        Variables exported

      totcharge

      Total charge of selection


    • size

      #to tell the extension of atoms selected

      tell size  select="segn PROA"

        Variables exported

      Xext, Yext, Zext

      X,Y,Z extension

      Xavg, Yavg, Zavg

      The geometric center


    • center

      #to tell the center of extension of atoms selected

      tell center  select="segn PROA"

        Variables exported

      Xce, Yce, Zce

      X ,Y, Z component of center respectively


    • ccenter

      #to tell charge center of atoms selected

      tell center  select="segn PROA"

        Variables exported

      Xce, Yce, Zce

      X ,Y, Z component of mass center respectively


    • mcenter

      #to tell mass center of atoms selected

      tell center  select="segn PROA"

        Variables exported

      Xce, Yce, Zce

      X ,Y, Z component of mass center respectively


    • orient

      #to tell orient of rigid of atoms selected

      tell orient  select="segn PROA"

        Variables exported

      Xev, Yev, Zev

      Eigen values

      Xax1, Yax1, Zax1

      Principal axis

      Xax2, Yax2, Zax2

      Secondary axis

      Xax3, Yax3, Zax3

      Tertiary axis

      Xce, Yce, Zce

      Mass center


    • contacts/nears

      #to tell near atoms around atoms selected except bonded contacts

      tell contact cut=2.0 select="segn PROA"

      #tell first atom information if found

      if($ncontacts>0) {

        tell atom select=¡±atom $segn $iseq $atname¡±

      }

        Variables exported

      Ncontacts

      Number of near atoms found

      Segn

      Segment name of first atom found

      Iseq

      Residue sequence index of first atom found

      Resn

      Residue name of first atom found

      Atname

      Atom name of first atom found

    • contactsAmong

      For finding overlapped, or closed contacted among selections except bonded contacts.

      #to tell number of closed contacts among all OH2 atoms

      tell contactamong cut=2.0 select="name OH2"

      #tell first atom information if found

      if($ncontacts>0) {

        tell atom select=¡±atom $segn $iseq $atname¡±

      }

       
        Variables exported

      Ncontacts

      Number of closed contacts found

      Segn

      Segment name of first atom found

      Iseq

      Residue sequence index of first atom found

      Resn

      Residue name of first atom found

      Atname

      Atom name of first atom found


    • box/boxsize

      #to tell the PBC box of MD system

      tell box

        Variables exported

      boxType

      Box type

      boxVol

      Volume of box

      boxA, boxB, boxC

      Box length A,B,C respectively

      boxAlpha,

      boxBeta,

      boxGamma

      Box angle Alpha, Beta, Gamma respectively


    • bestFFTdim

      #to tell the best dimensions for PME Fourier transform

      tell bestfftdim

        Variables exported

      fftX, fftY, fftZ

      X, Y, Z dim


    • density

      #to tell the density of MD system

      tell bestfftdim

        Variables exported

      density

      Density in g/cm of MD system

      volume

      Volume of MD system


    • volume

      #to tell accessible volume of selection

      tell volume rprob=1.4 select=¡±segn PROA¡± gridsize=1.0

        Variables exported

      molvol

      Volume of atoms occupied



    • unknownResidue/unknownResidueType

      #to tell unknown residue types in the structure

      tell unknownresiduetype selection=”ALL”

        Variables exported

      nresun

      Number of unknown residue types in selection

      resun

      Unknown residue types (residue types not defined in force field)

      unresn[nresun]

      Unknown residue names in array whose index start from 0


    • nmodel

      #to tell models counts for a multi-models PDB file

      tell nmodel file=”1LMV.pdb”

        Variables exported

      Nmodel

      Number of models found in the PDB file


    • istep

      #to tell the restart file state

      tell istep file=¡±run.rst¡±

        Variables exported

      istep

      The MD step of the restart state stored


    • trjsize

      #to estimate the trajectory size will be

      tell trjsize [nstep=5000000]

        Variables exported

      sizePerfrm

      The size of a frame in kb

      sizePerNs

      The size for a ns simulation

      Sizetot

      The total size for nstep simulation


    • msfInfo

      #to tell the summary of current structure

      tell msfinfo

        Variables exported

      Nseg

      Number of segments in the system

      Nres

      Number of residues in the system

      Natom

      Number of atoms in the system

      Nbond

      Number of bonds in the system

      Nangl

      Number of angles in the system

      Ndihe

      Number of dihedrals in the system

      Nimpr

      Number of improper dihedrals in the system

      Ncmap

      Number of cross terms in the system

      nimgroup

      Number of image operating groups

      netcharge

      Total charger of the system

      totmass

      Total mass of the system

      Xce

      component X of mass center

      Yce

      Component Y of mass center

      Zce

      Component Z of mass center

      Xavg

      X value of geometric center

      Yavg

      Y value of geometric center

      Zavg

      Z value of geometric center

      Xex

      System extension in X axis

      Yex

      System extension in Y axis

      Zex

      System extension in Z axis


    • ffInfo

      #to tell the summary of force field

      tell ff_info
        Variables exported

      Nrest

      Number of residue types in the force field

      Nprest

      Number of patching residues in the force field

      Natomt

      Number of atom types in the force field

      Nbondt

      Number of bond types in the force field

      Nanglt

      Number of angle types in the force field

      Ndihet

      Number of dihedral types in the force field

      Nimprt

      Number of improper dihedral types in the force field

      Ncmapt

      Number of cross term types in the force field

      Nvdwt

      Number of VdW types in the force field

      Nvdwpt

      Number of VdW pair types in the force field


    • pid

      #to tell the process ID

      tell pid

        Variables exported

      Pid

      The process id of current Modar instance


    • pot

        Only valid after energy subroutine called, i.e. valid after command "runmd","energy","domin"

        ...

        runmd

      #to print total potential energy of MD system for the last step

      tell pot

       
        Variables exported

      Pot

      The total potential energy of MD system


 

 

 

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