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
. 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
| (11) |
where <ampl>
is given in
and <freq>
in
.