IBIsCO
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**control**
This
is the file that contains the general parameters for the simulation (time
step, ensemble, thermodynamic conditions …).
specify which ensemble you want to use for simulation. Current option include three types micro canonical (NVE), canonical (NVT) and isobaric-isothermal (NPT) ensemble.*Ensemble:*
initial temperature in Kelvin (attention this temperature is used for thermostat and also for calculating the forces and potentials by Bolzmann inversion).*Temperature:*
initial pressure in kPa (target pressure in NPT ensemble).*Pressure:*
total number of atoms included in the system.*Natoms:*
the total number of time steps of the simulation.*Nsteps:*
the simulation time step in ps.*DT:*
thermostat coupling time in ps.*TAUT:*
pressure relaxation time in ps.*TAUP:*
isothermal compressibility (1/kPa).*BETA:*
the cutoff distance for non-bonded interaction in nm.*Cutoff:*
the distance in nm up to which pairs of particles are included in the neighbor list.*Neighbor_list_cutoff:*
number of time steps between updating the neighbor list.*Update_neighbor_list:*
number of time steps between printing the instantaneous values.*Nsampling:*
number of time steps between writing the trajectory file.*Ntrajectory:*
number of time steps between putting the net momentum equal to zero.*Halt_Drift:*
number of time steps between calculating the averages and printing the restart file.*Naverage:*
in this program there are two possible definitions of non-bonded pairs within the same molecules: atoms separated by more than three bonds ('1..5' interactions and above) or atoms separated by more than two bonds ('1..4' interactions and above).*Non-Bonded:*
in this program there are two options to define the bond and bend interactions. You can prepare Gaussian file and specify the Gaussian functions that are fitting to the bond length and angles distributions, or you can prepare the potential tables for bond and bend interactions.*Interaction:*
in this option you clarify that program must use the velocities are given in the initial coordinate file (NO) or initialize the particle velocities according to a Maxwell-Boltzmann distribution (YES).*Reset_velocities:*
number of processors in X direction. This number must not be less that two.*NPX:*
number of processors in Y direction. This number must not be less that two.*NPY:*
number of processors in Z direction. This number should not be less that two. In this program, one of the processors is assigned to write the output files. Then total number of processors that you need to run the program will be NPX+NPY+NPZ+1.*NPZ:*
This program is using a domain decomposition strategy to use a parallel machine. To calculate the non-bonded interaction each processor needs to receive the boundary region from neighbor processors. In this case the width of boundary region is our cutoff, but some time after mapping from atomistic to coarse graining supper atoms are so far, and to calculate the bonded part of forces and potentials (angle and torsion) you need to use a bigger number for boundary width to receive all information from boundary processors.*Boundary:*
**coordinate**
This
file contains the coordinates, the velocities and the connectivity table.
- Comment
- Time: previous simulated
time
- Comment
- Box length for X, Y, and Z
directions in nanometer
- Comment (5 lines)
- Total number of molecules.
- Total number of atom in the
molecule + Comment (Atoms_in_Molecule_No.) + index of the molecule.
- For each atom in the
molecule, specify the index of the atom, type of the atom (correspond
to the atom type in the interaction file), number of other atoms
connected to this one, coordinate (Sx, Sy, Sz), velocity (Vx, Vy, Vz)
and indices of the connected atoms. (The connectors (bonds) are
specified twice: one time for each of the two atoms forming the
connection.).
**interaction**
This
is the file that contains types of atoms, mass and different type of bonds,
angles, torsions and non-bonded interactions. In this file you have to
specify the name of the potential files for bonds and angles, if you want to
use the table for these interactions, and also the name of the tabulated
potential file for the different type of non-bonded interactions.
- Arbitrary title
- The number of different atom
type (attention the expression after this number is a keyword and must
not be changed).
- Comment
- For each atom type, specify
the arbitrary type number, atom label and mass (in
*g/mole*).
- The number of different of
types of bonds
- Comment
- Specify the atom types for
each type of bond. If you want to use the potential table for bond
interaction, you should put the name of files after the atom types. If
you don't want to use tabulated potential, don't put any things after
the bond types.
- The number of different
types of bond angles.
- Comment
- For each type of angles,
specify the atom types that form the angle. If you want to use the
potential table for bend interactions, put the names of corresponding
files after the atom types. If you don't want to use tabulated
potential, don't put any things after the angle types.
- The number of different
types of torsions.
- Comment
- For each type of torsions,
specify the atom types and name of the potential table.
- The number of non-bonded
interactions.
- Comment
- The atom types that are
belong to each kind of non-bonded interactions, and the name of
potential table.
The position of atoms on
the continuous chain is saving on the - Calculate the scaled
positions
**R**(t) of the atoms of the chain within the primary cell, i.e. all the components of the**R**(t) lie between ±*Box-Length/2*, using the following sequence of operations:
where by INT we refer to the FORTRAN
function which returns the integer part of the expression in the bracket. - Make the neighbour list (if
necessary).
If
the size of the box is bigger than three times the neighbour list cut off, we
use a link cell algorithm to make the neighbour list. The simulation box is
divided into cubic cells with the neighbour list cut off length, and instead
of the looking for the neighbour atoms in the whole box, searching is
restricted to the neighbour cells. If the box size is smaller, the neighbour
list update is performed by searching all possible atom pairs. All bonded
atoms are excluded from the neighbour list. - Calculate the bonded and
non-bonded interactions.
The
non-bonded part of the force is calculating by looping over the neighbour
list. The contribution of the force
where R - _{i}R is the relative poison vector of
the atoms _{j}i and j, and the double sum is over the all
interaction pairs. At this point we are storing the total non-bonded force on
each atom in a second vector f(t). To calculate the bonded part of
the force, we are making a loop over all the atoms, and for each atom, over
all bonds, angles and torsions to which the atom belongs. The bonded part of
the virial tensor is calculated using the position of atoms on the continuous
chain:_{nb}
where - Update the positions and
velocity of the atoms.
If
constant temperature conditions are used (NVT, NPT):
where τ
v(t - 1/2∆t) and the _{i}v(t + 1/2∆t):_{i}
The on-step temperature is calculating by means of
where N
Now, we can calculate the total pressure tensor:
- Reset the net momentum to
zero.
- Calculate the new volume and
scale the positions (in NPT ensemble).
where τ - Calculate the average of
parameters and print the restart file
- Store the trajectory file
- Sample
The basic choice for the
reduced units (indicated by an asterisk) is the following: - Unit of length, 1 nanometre
(Rscale)
- Unit of energy, k
_{B}×300 (Escale) - Unit of mass, atomic mass of
carbon (Mscale)
and from these basic units, all other units follow (time, pressure and
temperature).
In
IBIsCO, there are two options to define the bond and bend interactions. You
can prepare the Gaussian file and specify the Gaussian functions that have
been fitted to the bond lengths and angle distributions, or you can prepare
potential tables for bond and bend interactions. The strategy to calculate
the potential and force during the simulation is the same for both options.
We are using liner interpolation to find the forces and potentials. In the
case of GAUSSIAN we need to make the force and potential tables at the start
of the simulation. Given a distribution P(θ) of some structural parameter θ, the corresponding potential is derived by a simple
Boltzmann inversion of P(θ). The corresponding potential, V(θ), obtained by Boltzmann inversion is written as follows: where k If we define
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