Yammp Shell
Introduction
Simple Commands
Modify the Molecular Environment
Modify the Linesearch Methods for Energy Minimization
modify linesearch
   method which      # 1
   #
      iterations value  # 2
      min_grad ming     # 3
      tolerance tol     # 4
      step_size step    # 5
      min_step mins     # 6
      max-step maxs     # 7
   end

Modify the line search methods. The linesearch methods are used by the conjugate gradient energy minimization methods. These values should be modified only with great care. The minimizers are very sensitive to these settings. (1) which specifies a line search method which can be the davidon cubic interpolation method (preset value), the powell parabolic search method or nosearch which actually is a heuristic method. Normally you should stick to the Davidon method which is fast but is unstable when far from the minimum. The Powell method is more tolerant of bad initial state but convergence is extremely slow. The heuristic search method should be used only as a last resort.

The other settings are in unusual (internal) units of measurement; the only recommendations here are to ignore the units and adjust the numbers by increasing or decreasing the exponents by one at a time. (2) Maximum number of linesearch iterations, preset value is 10. (3) Root Mean Square (RMS) gradient tolerance in the Davidon method, preset value is 10-4 CEU/mol/Å. (4) Step tolerance in the Davidon method, preset value 10-4 Å2/CEU. (5) Initial step size, preset value 10-7 Å2/CEU. (6) Minimum step step size in the Powell method, preset value 10-5 Å2/CEU. (7) Maximum step size in the Powell method, preset value 10-3 Å2/CEU.


Modify the Energy Minimization Methods
Modify the Molecular Dynamics Methods
Modify the Monte Carlo Methods
Modify the Non-Bond Terms During a Simulation
Modify Bond Constraints for Molecular Dynamics
Modify the CONTRA-MD Method
Defining and Invoking Macros
Control Structures
Examples

 


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