Banner

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.
MAPS Logo 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.
References
  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
Company News

MAPS 3.2 has been released
MAPS 3.2 has been released on April 25, 2010. Quality by design is possible with MAPS 3.2 since it's modeling and simulation modules provide you with the information you need in order to focus experimental efforts and rapidly identify promising candidates. Discover how scientists in several industrial fields use Scienomics products and know how in order to innovate while controlling costs.

Scienomics and 3 other German companies for the NanoSISAM project
Nanotechnology is an expanding industry sector, withstanding also the current economic crisis...

MAPS 3.1 patch release
We are happy to inform you that MAPS 3.1® patch is ready for download

Whats new in MAPS 3.1
MAPS 3.1® introduces the Transition State Locator, a stand-alone module which can drive transition state searches with Abinit, MNDO and Turbomole using LST, QST and NEB methods.

MAPS 3.0 has been released
A new major version of the Materials and Processing Simulation Platform MAPS® has been released recently.

Toxicity, hazard and risks : how to comply with REACH regulation while controlling the associated costs?
Nancy, Paris and Verneuil-en-Halatte France; Munich, Germany - July 19, 2007

The French National Agency of Research (ANR) has recently selected the R&D project "Integration of decision analysis methods and predictive chemistry for assessment of toxicity (CANTO)" jointly submitted by SCIENOMICS and the Institut National de l'Environnement Industriel et des Risques (INERIS).

New web based services for Scienomics customers
Nancy and Paris, France; Munich, Germany - April, 20, 2007.

Customer satisfaction is for Scienomics the center of its concerns. In order to achieve an even higher quality of the services provided to our customers Scienomics launches an upgraded website. Through this new website customers can benefit a series of services such as a personalized space with important information about products they have acquired

Scienomics announces Materials and Processes Simulations - MAPSŪ platform 2.1 is released

Scienomics in a constant effort to achieve higher customer satisfaction announces the release of MAPS 2.1®.

MAPS® is the leading integration platform for open source, proprietary and third party molecular simulation engines.

Scienomics announces Materials and Processes Simulations - MAPSŪ platform 2.0 is released
Nancy, Paris, France; Munich, Germany - August 16, 2006.

Scienomics is pleased to announce the release of MAPS® 2.0. With this new release MAPS is entering a completely new field of simulations, the powerful arena of mesoscale modeling.

Scienomics announces Materials and Processes Simulations - MAPSŪ
Nancy, Paris, France; Munich, Germany - February 16, 2006.

Scienomics, a software and services company for molecular modeling, is pleased to announce that Materials and Processes Simulations - MAPS® platform v1.6 is released.

Scienomics launches the Innovative Modeling Technology Consortium.
Nancy, Paris, France; Munich, Germany - January 2, 2006. Scienomics, a software and services company for molecular modeling, is pleased to announce the launch of the first phase of its Innovative Modeling Technology (IMT) Consortium.

Scienomics announces the release of Materials and Processes Simulations - MAPSŪ
Nancy, Paris, France; Munich, Germany - December 16, 2005.

Scienomics, a software and services company for molecular modeling, is pleased to announce that Materials and Processes Simulations - MAPS® platform 1.5 is released. MAPS® is Scienomics' premier software platform for carrying out materials modeling and simulations. Developed by Scienomics software engineers, MAPS® provides a flexible framework for accessing both proprietary and open source simulation codes. MAPS® is a flexible and customizable environment geared towards the molecular modeling for the chemicals, pharmaceuticals and materials industries. MAPS® serves as an integration tool for all modeling related tasks and data and offers a multi-project modeling environment on major operating systems (currently on Linux, Windows).

Scienomics is holding the 1st Innovative Modeling Technology Consortium meeting
Nancy, Paris, France; Munich, Germany - September 8, 2005.

Scienomics is holding its first Innovative Modeling Technology Consortium (IMT Consortium) seminar on September 8 - 9, 2005 in Paris, France. During this two day event scientists from leading companies from the Chemicals, Petrochemicals and Personal Care industrial segments will discuss together with Scienomics staff and Scienomics advisors the content of Scienomics'

Scienomics announces Materials and Processes Simulations - MAPSŪ platform
Paris, France - December 16, 2004.

Scienomics, a software and services company for molecular modeling, is pleased to announce that Materials and Processes Simulations - MAPS® platform 1.0 is in beta testing. Currently about 5 research groups world-wide participate in this beta testing phase.

Scienomics announces the 1st release of Materials And Processes Simulations
Scienomics, a software and services company for molecular modeling, is pleased to announce that it will be releasing the first version of its platform for Materials and Processes Simulations (MAPS®) in fall 2004.

Foundation of Scienomics
Paris, France, April 12, 2004.
Scienomics, a software and services company in the area of molecular modeling is founded. Scienomics is a young and dynamic company based in Paris, France, dedicated to providing its industrial.


News 1 - 16 of 16
 First | Prev. | 1 | Next | Last | Paged

MAPS Gallery