Applications of Ascalaph Designer Software

Ascalaph Designer is a general-purpose molecular modeling computer program for molecular design and simulation. Programs are represented in a single graphical environment as their own implementation of molecular dynamics as well as popular classical and quantum mechanical methods. It provides a graphical environment for the common quantum and classical molecular modeling programs ORCA, NWChem, Firefly, CP2K and MDynaMix. Molecular mechanics calculations cover model building, energy optimization, and molecular dynamics. Firefly (formerly PC GAMES) covers a wide range of quantum chemical methods. Ascalaph Designer is free and open-source software released under the GNU General Public License version 2 (GPLv2). Some of Ascalaph Designer's capabilities include molecular graphics, molecular model building, molecular dynamics, molecular geometry optimization, quantum chemistry, multi-time-step integration, fourth-order integration, supercomputer computing with MDynaMix, flexible SPC water models, and implicit water Model.

Our Services Based on Ascalaph Designer Software

On the Ascalaph Designer software platform, CD ComputaBio can provide customers with high-quality computational biology services.

• Building Crystal of Polymers, Nanotubes and Proteins
  Scientists at CD ComputaBio use Ascalaph Designer to build crystal structures of polymers, nanotubes, proteins, and nucleic acids. The program includes Crystal builder, which generates regular lattices from molecules by spatial replication of the model. Lattice can be generated by setting lattice parameters or lattice vectors.
• Editing Chains of Proteins and Nucleic Acids
  Chain editors are the primary tool for generating molecular models. It allows building chain molecules from predefined residues. We utilize Ascalaph Designer's chain editor for editing proteins and nucleic acids are large chain structures that require special construction tools due to their size, regular structure, and scientific importance.
• Molecular Dynamics
• Scientists at CD ComputaBio perform molecular dynamics calculations of protein, DNA, RNA, and enzyme by in-house methods or external programs. MDynaMix allows parallel computing on clusters of supercomputers and workstations.
• Quantum Calculations
• Energy calculations
  On the basis of the chemically optimized structure, we use a larger basis set for single-point energy calculations (we take the structure obtained in the optimization step as the initial structure. The single-point energies of the two conformations are calculated under the larger basis set)
• Optimization
  We use semi-empirical calculations to generally correct for severe geometric violations of molecular structure. Therefore, semi-empirical optimization is a routine task after the mouse has drawn molecules.
• Properties calculations
  Since the quantum mechanics module is included in the molecular mechanics package, electrostatic calculations are of particular interest. Our scientists use this software for molecular electrostatics and dipole moment calculations.

The Features of Ascalaph Designer Software

• Ascalaph Graphics is a basic graphical interface module that provides main window design, 3D graphics, information windows and error message windows.
• Ascalaph Quantum provides interaction with the quantum mechanics program PC GAMESS.
• Ascalaph Designer provides methods for building and editing molecular models, geometry optimization, and molecular dynamics simulations.
• Ascalaph Liquid is a hardware-accelerated version of Ascalaph Designer.

Our Capabilities

On the Ascalaph Designer software platform, our scientists can provide our customers with molecular simulation, building crystal, structure optimization, geometry optimization and chemical force field development.