Modar internal command:

 doMin/minimize

To do an energy minimization for whole MD system, currently Modar supports three types minimization method: Steep Descent (SD), Steep Descent with Monte Carlo(SDMC), and Steep Descent with a fuse (SDFuse). SD only may not work for a poor initial structure, SDMC is good but may take more time to reach local minimal state, SD should be the first choice for the final stage minimization.

  • Syntax and examples

    # do a 100 step SDFuse minimization

    domin method=SDFuse nstep=100 nprint=1 ftol=1e-5 fuse=0.2 \

          enefile="mini.ene" frqene=1 \

          trjfile="mini.trj" frqtrj=1

     

    # do a 100 step SDMC minimization

    domin method=SDMC   nstep=100 nprint=1 ftol=1e-5 iseed=314159 \

          enefile="mini2.ene" frqene=1 \

          trjfile="mini2.trj" frqtrj=1


  • Keywords

    Method=<type name>

    Available methods are SD, SDMC, SDFuse (default value)

    nstep=<int>

    How many cycles to run

    Etol=<real>

    Energy tolerance, default value is 0

    Ftol=<real>

    Force residue tolerance, default value is 0

    Htol=<real>

    Move stride tolerance, default value is 0

    Hstep=<real>

    Initial move stride, default value is 0.02 Angstrom

    Fuse=<real>

    The fuse of energy overflow for SDFuse method, default value is 0.2 (20%), which is a good value for regular system.

    Nprint=<int>

    Energy print out frequency

    Trjfile=<filename>

    To tell the trajectory file name

    Trjfmt=<type name>

    Trajectory file format, only Modar or Charmm available currently

    Frqtrj=<int>

    Trajectory write out frequency

    Enefile=<filename>

    To tell the energies profile file name

    Frqene=<int>

    Energies profile write out frequency

  • Variables exported
    none


 

 

 

 

 

 

 

 

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  Email: support@beemd.org

 

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