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FQS Poland – SCIGRESS

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SCIGRESS

SCIGRESS is molecular design modeling software currently available for Microsoft Windows XP or Vista. A state-of-the-art molecular builder and visualizer enables the researcher to import experiment structures using a variety of industry standard formats, or to build novel structures using a multi-function tool palette. SCIGRESS has the unique ability to apply a wide range of computational models, from molecular mechanics through rigorous quantum electronic structure techniques, to all types of molecular systems, from organic molecules, to inorganics, polymers, materials systems (metals, oxides, ceramics, semiconductors), and whole proteins.

Screenshot SCIGRESS

SCIGRESS is a successor of Scigress Explorer (CAChe) and Materials Explorer and integrates both programs into one powerful suite.

Molecular mechanics calculations can be performed on organic and inorganic molecules containing all elements of the periodic table using variety of force fields. Force field parameters can be modified by the user. SCIGRESS includes CONFLEX for automated global minimum searching and systematic generation of low-energy conformers for molecules of any shape, including ring systems.

SCIGRESS provides vast and customizable modeling functions that allow precise control of simulation parameters of advanced molecular dynamics simulation methods that introduce an impressive set of real-world variables and conditions to in silico materials experiments. SCIGRESS enables users to set the simulation conditions, such as the number of simulation steps, the ensemble, and potentials, and take complete control of their modeling environment. Users can create their own templates for simulated systems and conditions, as well as set potential assignment rules.

Electronic structure methods in SCIGRESS include Extended Hückel theory (for all elements), ZINDO and MO-S (primarily for UV-visible spectra), and MO-G (previously MOPAC). MO-G, a refinement of MOPAC developed by Fujitsu scientists, covers all main group elements and many metals, with an extensive choice of models including PM6, PM5, AM1, PM3, MINDO/3, and MNDO. It also includes the COSMO solvent model and d-orbitals for transition metals. SCIGRESS quantum chemistry methods facilitate the study of kinetics and thermodynamics, and the prediction of many physical and chemical properties.

SCIGRESS can transparently run and visualize results from the third party programs: ADF, GAMESS, Gaussian, PHASE, MOPAC2009, and CONFLEX6.

Ready for large systems SCIGRESS can easily interface with large-scale multiprocessor servers to run high performance calculations for very large systems. Highly parallelized compute engines are available for such applications.

If you have further questions, need a trial version or an offer, contact us via Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein! or by phone +49 (0) 61 72 - 59 05 - 131.

Features

SCIGRESS
  • Determination of total energy (DFT), heat of formation (semi-empirical methods) or strain energy (MM).
  • Reaction mechanism determination via transition state searching and evaluation and visualization of intrinsic reaction coordinates.
  • Determination of low energy conformations.
  • Vibrational analysis including visualization of IR spectra and normal modes of vibration.
  • Interactions with radiation including visualization of UV-visible spectra, and identification of molecular orbitals, electron densities, and electrostatic surfaces.
  • Molecular dynamics study and analysis of phase transitions, expansion, defects, compressibility, tensile strength, adsorption, absorption, and thermal conductivity.
  • QSAR/QSPR analysis.
  • Protein-ligand docking.
  • Quantum chemistry of full proteins.

Research Tools

Tools available to the reseachers for analyzing molecular structure and properties include the following:

  • Reaction mechanism determination via determination of reaction transitions states and evaluation and visualization of intrinsic reaction coordinates.
  • Determination of low energy conformations.
  • Vibrational analysis including visualization of IR spectra and normal modes of vibration.
  • Interactions with radiation including visualization of UV-visible spectra, and identification of molecular orbitals responsible for orbitals electronic transitions.
  • 3D-visualization of electronic surfaces including orbitals, electron densities, and electrostatic surfaces.
  • Study of phase transitions, expansion, defects, compressibility, tensile strength, adsorption, absorption, thermal conductivity.
  • Visualization of experimental crystal and protein structures.

Computational tools implemented in SCIGRESS

  • Molecular Mechanics
    Mechanics is used by SCIGRESS to optimize molecular structures using an augmented version of Allinger's standard MM2 and MM3 classical force field.
  • Dynamics
    Dynamics methods use classical, empirical force fields to approximate the movement of atoms. The dynamics application uses the same force fields (MM2 and MM3) as the Mechanics application. Use dynamics to visualize conformations that occur as a result of molecular motion; discover information regarding the structure-energy relationships of the molecule; investigate conformational space occupied by the system at varying temperatures.
  • Molecular Dynamics (MD-ME)
    MD-ME is an advanced molecular dynamics module that can be used to study the molecular dynamics of model systems including crystals, polymers, dendrimers, etc. MD-ME implements a wide variety of force fields that can be used with organic and non-organic models.
  • MO-G (MOPAC)
    MO-G is a general-purpose semi-empirical molecular orbital package. Use MO-G to calculate the vibrational spectra, thermodynamic quantities, isotopic substitution effects and force constants for molecules, radicals, ions, and polymers. For studying chemical reactions a transition state location routine is also available.
  • CONFLEX
    CONFLEX generates low energy conformers of a molecule of any shape. Use CONFLEX to compute optimum geometries, conformations and potential energy maps.
  • ZINDO
    ZINDO computes semi-empirical quantum mechanical values for molecular properties and spectra of molecules. ZINDO uses theoretically-based INDO parameterization and therefore contains parameters for more elements than does the experimentally-based MO-G or MO-S. However, because MO-G has been specifically parameterized for ground-state heats of formations MO-G is the better method for computing molecule structures and energetics. Use ZINDO to carry out calculations of electronic UV-visible absorptions spectra.
  • MO-S (MOS-F)
    MO-S is a semi-empirical program with advanced methods (configuration interactions and random phase approximation) for evaluation of UV-visible electronic absorption spectra. Use MO-S for the evaluation and interpretation of electronic structure transitions.
  • Extended Hückel
    Extended Hückel is a semiempirical quantum mechanical method used for calculating the electronic wavefunction to determine electron densities, molecular orbitals, electrostatic potentials, partial charges and bond orders.
  • QSAR & QSPR Module
    SCIGRESS combines experimental data with over 100 descriptors to develop QSAR protocols, and additional descriptors can be defined within the system.

Computational tools interfaced to SCIGRESS

  • ADF
    ADF is developed and released by Scientific Computing & Modelling NV (SCM).
  • GAMESS
    GAMESS is developed and released by the Gordon Group at Iowa State University. Please refer to www.msg.chem.iastate.edu/gamess for details on how to obtain the program.
  • Gaussian
    Scigress Explorer can transparently run and visualize results from the third party program Gaussian. Gaussian is not included in the package. Scigress Explorer works with Gaussian 03W revision B.03 or higher.
  • Advance/PHASE
    Advance/PHASE is developed and released by AdvanceSoft Corporation. Please refer to www.advancesoft.jp for more information.
  • MOPAC2009
    MOPAC2009 is developed and released by Stewart Computational Chemistry. Please refer to www.openmopac.net for details on how to obtain the program.
  • CONFLEX6
    CONFLEX is developed and released by CONFLEX Corporation. Please refer to www.conflex.us for details on how to obtain the program.

Model Builders

SCIGRESS provides wizards to aid in the development of unit cells targeted at molecular dynamics simulation investigations. SCIGRESS Model Builders include:

  • Random Cell enables you to create a Molecular Dynamics (MD) cell with a mixture of various kinds of atoms and molecules that are randomly configured.
  • Template Cell enables you to create a crystal structure MD cell by making use of an existing template which incorporates the fractional coordinates of (atomic) positions and the cell parameters.
  • Interface Cell enables you to add juxtapose MD cells together in any direction.
  • Liquid Crystal Cell enables you to create a liquid crystal structure MD cell by configuring liquid crystal molecules in a particular phase.
  • Homopolymer enables you to build a unit cell containing homopolymers using a monomer in which the head and tail atoms have been defined.
  • Block Polymer enables you to build a unit cell with two or more segments of polymers in which the head and tail atoms have been defined.
  • Random Polymer enables you to build a unit cell that contains two or more different polymers randomly arranged.
  • Homodendrimer enables you to build a unit cell containing a dendrimer repeating the same dendrimer monomer.
  • Random Dendrimer Builder enables you to build a unit cell by generating a random dendritic structure from multiple dendron monomers.
  • Infinite Chain Builder enables you to configure infinite chain molecules along the c-axis in a unit cell.
  • Amorphous Cell enables you to construct unit cell containing an amorphous state of polymers built with Polymer Builder.
  • Random Polymer Cell enables you to build a unit cell containing random polymers.

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