System

• Molecule_types   <num_types>
  <name> <number>  [fixed]
  ...
  <name> <number>  [fixed]
  

  Which molecules to simulate. <num_types> is the number of molecule types. This keyword must be followed by <num_types> lines each of which contains at least two parameters: <name> and <number>

  <name> - name of the molecule. File <name>.mmol , describing the molecular structure and the force field parameters, must be present in directory specified by parameter Path_DB.

  <number> - number of molecules of this type.

  ``fixed'' - Option ``fixed'' signals that these molecules are fixed and will not move in the MD procedure.

  This keyword and its parameters (except ``fixed'') are compulsory

• PBC <type>

  Type of periodic boundary conditions

  <type> may be:

  rect - rectangular (default)

  hexa - hexagonal

  octa - truncated octahedron

• Box <box-x> <box-y> <box-z>

  Specifies simulation box size (in Å). In case of hexagonal boundary conditions, only box-x and box-z have a meaning. For octahedral boundary conditions only <box-x> has a meaning. The keyword cannot be used simultaneously with ``Density''

• Density <value>

  Setup initial density. <value> is density in $g/cm^3$. This option cannot be used simultaneously with setting up box sizes. In case of rectangular periodic boundary conditions, a cubic cell is implied. Zero density implies ``vacuum simulation'' regime with the box size automatically set to 1000 Å

• El_field <ampl> <freq>

  Put the system in a homogeneous time-dependent electrostatic field

  
  

  $$E(t) = A\cos(2\pi\omega t)$$ (11)

  
  

  where <ampl>$=A$ is given in $V/cm$ and <freq> $= \omega$ in $Hz$.