Modar internal command:

 trjCalc

It’s a extension of command "calc", which calculates distance, angle, dihedral and more , this one does the calculation loop over the trajectories fed and prints the result to file in MD time sequence rather than exporting variables.

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

  • General arguments

             Following arguments are shared for all subcommands.

    trjFile=<file name>

    Input trajectory files, each argument can only carry one file. Please note that files must be fed in sequence in MD time.

    Timestart=<real>

    To specify the MD time of the beginning frame, if not specified the first frame of the trajectories will be

    TimeEnd=<real>

    To specify the MD time of the end frame, if not specified the last frame of the trajectories will be

    Timestride=<real>

    The MD time stride in ps

    Output=<file name>

    The output file name, the result will be print to log file if it's not specified.

  • Subcommands and examples
    • zrgy

      #to compute radius of gyration, Z component only

      trjcalc zrgy select="segn ILC" \

              trjfile="equil.trj" \

              timestart=200 \

              timeend=500 \

              timestride=2 \ 

              output="zrgy.txt"


    • rgy

      #to compute radius of gyration for atoms selected

      trjcalc rgy  select="segn PROA" \

      trjfile="equil.trj" \

              timestart=200 \

              timeend=500 \

              timestride=2 \

              output="rgy.txt"



    • center

      #to compute center of mass of atoms selected

      trjcalc center  select="segn PROA" \

            trjfile="equil.trj" \

              timestart=200 \

              timeend=500 \

              timestride=2 \

              output="ce.txt"


    • orient

      #to compute center of mass of atoms selected

      trjcalc orient  select="segn PROA" \

      trjfile="equil.trj" \

              timestart=200 \

              timeend=500 \

              timestride=2 \

              output="orient.txt"



    • dist/distance

      #to compute distance between two groups

      trjcalc dist  select="reside PROA 1" \

              select="reside PROA 100" \

              trjfile="equil.trj" \

              timestart=200 \

              timeend=500 \

              timestride=2 \

              output="dist.txt"



    • dist2line

      #to compute distance to Z axis

      trjcalc dist2line lineOrg=”0,0,0” lineVec=”0,0,1” \

       select="reside PROA 1" \

              trjfile="equil.trj" \

              timestart=200 \

              timeend=500 \

              timestride=2 \

              output="dist.txt"



    • dist2plane

      #to compute distance to XY plane

      trjcalc dist2plane point=”0,0,0” vec=”0,0,1” \

       select="reside PROA 1" \

              trjfile="equil.trj" \

              timestart=200 \

              timeend=500 \

              timestride=2 \

              output="dist.txt"



    • Zcom

      #to compute Z distance between two groups

      trjcalc dist  select="reside PROA 1" \

              select="reside PROA 100" \

              trjfile="equil.trj" \

              timestart=200 \

              timeend=500 \

              timestride=2 \

              output="dist.txt"



    • Ycom

      #to compute Y distance between two groups

      trjcalc dist  select="reside PROA 1" \

              select="reside PROA 100" \

              trjfile="equil.trj" \

              timestart=200 \

              timeend=500 \

              timestride=2 \

              output="dist.txt"



    • Xcom

      #to compute X distance between two groups

      trjcalc dist  select="reside PROA 1" \

              select="reside PROA 100" \

              trjfile="equil.trj" \

              timestart=200 \

              timeend=500 \

              timestride=2 \

              output="dist.txt"



    • angle

      #to compute angle

      trjcalc dist  select="reside PROA 1" \

      select=¡±reside PROA 10¡± \

      select=¡±residue PROA 20¡± \

      trjfile="equil.trj" \

              timestart=200 \

              timeend=500 \

              timestride=2 \

              output="angle.txt"



    • dihe

      #to compute dihedral

      trjcalc dihe group1="atom PROA 49 C" \

      group2="atom PROA 50 N" \

      group3="atom PROA 50 CA" \

      group4="atom PROA 50 C" \

      trjfile="equil.trj" \

                 timestart=200 \

                 timeend=500 \

                 timestride=2 \

                 output="dihe.txt"



    • rmsd

      #to compute rmsd

      trjcalc rmsd fitgroup="segn PROA && name C CA N O" \

      calcgroup=¡±segn PROA¡± \

      trjfile="equil.trj" \

              timestart=200 \

              timeend=500 \

              timestride=2 \

              output="rmsd.txt"



    • rdf

      #calculate Radial Distribution for O-O

      trjcalc rdf cutoff=15.0 binSize=0.1 \

              reference="name O*"  target="name O*" startpos=1.5 \

              natomref=1 natomtar=1 \

              trjfile="step4_equil.trj" \

              timestart=$ts \

              output="rdf_O_O.txt"



    • numberalong

      #report distribution numbers along a line

      trjcalc numberalong

      trjcalc numberalongs  tart="0,0,-25" end="0,0,25" \

             select="resname so4*" \  

             naunit=5 stride=1



    • numberaroundaxis

      #calculate Radial Distribution around a line

      trjcalc numberaroundaxis org="0,0,0" vector="0,0,1" \

              select="resname so4*" naunit=5 cutoff=20 stride=1



    • numberaroundpoint

      #calculate Radial Distribution around a point

      trjcalc numberaroundpoint org="0,0,0" \

              select="resname so4*" naunit=5 cutoff=20 stride=1



    • hydrogenbond

      #report hydrogen bonds

      trjcalc hydrogenbond accepters="residue PROA 1" donors="resn TIP*" \

              len=2.5 th1=105 th2=105



 

 

 

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