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

• Combination_rule <type>

  Use another (than Lorentz-Berthelot) combination rule for Lennard-Jones parameters for different types

  type may be one of the following:

  Sigma_geom

  LJ $\sigma$ parameter is calculated as a geometrical average of the both types (as for example in the OPLS force field)

  Kong

  use Kong rules (J.Kong, J.Chem.Phys., 59, 2464, (1973))

  Fender

  use Fender-Halsey rules ( B. E. F. Fender and G. D. Halsey, Jr. "Second Virial Coefficients of Argon, Krypton, and Argon-Krypton Mixtures at Low Temperatures", J. Chem. Phys. 1881 (1962))

  Waldman use Waldman-Hagler rules (M. Waldman and A. T. Hagler "New combining rules for rare-gas Van der-Waals parameters", Journal of Computational Chemistry 14 pp. 1077-1084 (1993))

  Mixed use mixed combination rules from paper: A. Nikitin, Y. Milchevskiy, A. P. Lyubartsev "AMBER-ii: New Combining Rules and Force Field for Perfluoroalkanes" J. Phys. Chem. B, 119, 14563-14573 (2015)

  Default: use Lorentz-Berthelot combination rules

• Pair_list [FF_file] <file_name>

  Introduce special Lennard-Jones parameters for pairs of atoms given in file <filename>.

  Without FF_file option the list of pairs is directly composed from the site numbers given in file <filename>. Each non-commentary line of this file consists of two integer numbers specifying the global site numbers of two atoms, followed by two real numbers having the sence of LJ parameters $\sigma$ and $\varepsilon$ for the given pair of sites, and eventually followed by two other real numbers which are LJ parameters $\sigma$ and $\varepsilon$ for 1-4 bonded interactions. This list overwrites the Lennard-Jones parameters defined by the combination rules and eventually modified by parameters in the .mmol files.

  If option FF_file is given, the list of pairs is composed from the LJ_PAIRS section of the force field file given by parameter <filename> (same force field file as used by the makemol utility). The pairs of atoms with force field atom types (given by the 9-th colomn of the .mmol files) which match atom types in the LJ_PAIRS section of the force field file are included into the list of pairs for special Lennard-Jones interactions.

• 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 $Hz$.

• G-force <type> <g-force>

  A gravitation-like force (acting along Z-axis on each atom proportionally to its mass) is added for molecules of type <type>. Parameter <g-force gives the value of acceleration $g$ in $10^{12} m/s^2$. The force can be applyed for several molecular types, is this case the keyword should be repeated for each type.