AMORPHOUS BUILDER

A brief Outline of the Algorithm

A molecule is considered as a sequence of particles with a well defined connectivity. The position of a simple atom is defined by its Cartesian Coordinates. If the atom belongs to a molecule there are alternative ways to define its position, by using: A unit vector and a bond length (for the 2nd atom of a molecule) A bond length, a bond angle and a rotational angle (for the 3nd atom of a molecule) A bond length, a bond angle and a torsion angle (Flory representation) A bond length and two bond angles (lateral atoms) The position of a group is defined by the Cartesian Coordinates of its atoms. If we consider the group as rigid, we can use a local frame in order to express the Cartesian Coordinates of its atoms. For the creation of this frame, we use the first three group atoms with the Ox axis laying together with the group first bond axis and the Oxy plane being the plane of these atoms.

Inserting atoms

• Insert the first atom of the molecule
A point in the simulation box is selected randomly. If there is no overlap the atom will be inserted otherwise we have to try a new position. The maximum number of trials in order to insert the particle is “Maximum Trials” parameter. If this number is exceeded, then the particle will be inserted in the lowest energy value position.
• Insert the second atom of the molecule
If the first particle is an atom, the locus will be a sphere centered on that atom, with radius equal to the bond length which is selected from the distribution. We select one point of the locus randomly. If there is no overlap/concatenation, the atom will be inserted. The maximum number of trials in order to insert the particle is “CB trials” parameter. If this number is exceeded, the particle will be inserted in the lowest energy value position (where there is no concatenation).
• Insert the third atom of the molecule
Given the first bond of the chain, one angle and one bond length are selected from the appropriate distributions. The locus of the atom will be a circle normal to the bond vector and with its center lying on the vector line. A point of the locus is selected randomly. If no overlaps/concatenations exist the atom will be inserted. The maximum number of trials in order to insert the particle is the “CB trials” parameter. If this number is exceeded, then the particle will be inserted in the lowest energy value position (where there is no concatenation). In a very similar fashion we can insert the following atoms, and the algorithm is also capable of inserting whole groups of atoms in one step. During the building process a concatenation check is performed.

A PDF datasheet for Amorphous builder is available here

System requirements

• MAPS is running on Linux and Windows XP operating systems.
• Amorphous Builder is incorporated in MAPS and runs on the same platforms as MAPS.

1. D. N. Theodorou, U. W. Suter, Macromolecules, Vol. 18, No. 7, p. 1467, 1985
2. D. Frenkel, G. Moij, B. Smit, J. Phys. Condens. Matter, 3, 1991, 3053 f.
3. J. I. Siepmann, D. Frenkel, Molec. Phys., Vol. 75, p. 59, 1992
4. J. de Pablo, M. Laso, U. Suter, J. Chem. Phys. 96(3), 1992, 2395 f.
5. T. J. H. Vlugt, M. G. Martin, B. Smit, J. I. Siepmann, R. Krishna, Molec. Phys., Vol. 94, No. 4, p. 727, 1998