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FUJITSU Technical Computing Solution SCIGRESS

SCIGRESS
  • An integrated platform for computational chemistry to support the development of materials
  • Equipped with a rich variety of modeling functions, computational engines, and analysis functions
  • Highly expandable with the ability to plug-in a wide variety of computational programs
  • Can be used without having to designate a particular machine within a network by using a “network license”

An integrated platform that can flexibly work together with a wide variety of computational methods

High precision

New Hamiltonians (PDDG/NDDO method, RM1 method) have been added to 
the semiempirical molecular orbital engines “MO-G” and “MO-S”. These increase the precision of heat of formation computations by 25% compared to PM3 when using the PDDG/NDDO method, and by 48% compared to AM1 when using the RM1 method.
A function for interfacing with the “MOPAC2007” semiempirical molecular orbital method software that supports the high-precision density functional software “ADF”, “PHASE”, and the PM6 method has also been added.
These high-precision partner products can be used in SCIGRESS.

Increased speed

The speed and convergence of structural optimization using the "MO-G" and "MO-S" semiempirical molecular orbital methods has been increased up to a maximum of 6 times through the addition of the GDIIS*1 method.
Furthermore, efforts continue to be made in SCIGRESS to support multi-core CPUs and improve the efficiency of parallelization.

1: Geometry optimization using Direct Inversion of the Iterative Subspace

Effective utilization of parallel distributed computational resources

SCIGRESS is equipped with a job management function. This ensures maximal utilization of the computational resources you own by automatically allocating jobs to idle CPUs.
The new addition of network licenses makes it possible to execute high-speed parallel computations without knowing the location of a computer.

Expandability

SCIGRESS employs a highly expandable API. This delivers integration not only with partner products "ADF" and "PHASE", but with other well-known computational programs such as "Gaussian", "GAMESS" and "LAMMPS".
We also have a service for porting any software you desire to SCIGRESS, so please feel free to contact us in this event.

Usability

The various modeling tools for creating molecular structures from small molecules to large molecules and crystal structures are shared within the platform, making it possible to operate a variety of application software from a unified GUI.

Increased efficiency using procedures

Multi-step procedures such as executing calculations using the more detailed density function method after structure optimization using the molecular orbital method can be easily edited and executed.
This speeds up the research and development process by improving the efficiency of work such as by allowing simulations and experiments to proceed in parallel.

Covers all aspects of leading edge research from building models to computation and analysis

Workspace (Model Builder/Result Viewer)

Workspace is a module for building molecules. These can be built easily simply by using the mouse. It also shows molecular orbitals, electrostatic potential energy maps, UV-Vis spectra, and IR spectra from the calculation results.

WorkspaceWorkspace

Electron density surface

Electron dinsity surface
  • Color-coded by electrostatic potential
  • Color-coded by frontier electron density
  • Color-coded by order of reactivity

etc.

Electrostatic potential surface

Electrostatic potential surface

Molecular orbital

Molecular orbitalMolecular orbital

Spreadsheet (Automated Batch Computation GUI)

  • Spreadsheet makes it possible to use lists to manage the large amounts of compounds and computation results synthesized in a laboratory.
  • Automatic calculations can be executed on batches of multiple compounds by specifying in advance the properties you want to find.
  • Sorting, graphing, and linear regression of data can be performed easily. Data can be output in a format suitable for submitting journal papers.
  • This alleviates much of the effort involved in calculations.

 Spreadsheet

Spreadsheet

Calculation Modules

Mechanics

This module is used for calculations such as the optimal structure of molecules using molecular mechanics methods.

Dynamics

This allows the behavior of molecular models to be simulated using molecular dynamics software.

Extended Huckel

This is an empirical molecular orbital calculation method that solves the Schrodinger equation.

ZINDO

This is a semiempirical molecular orbital program.

MO-G

This is a semiempirical molecular orbital program.

MO-S

Allows the ultraviolet and visible spectra of organic molecules to be determined to high precision.

MD-ME

This is software for aiding in the design of various materials composed of inorganic and organic materials based on classical molecular dynamics methods.

To calculation module list page

External Program Interface

  • An interface is provided for using the “PHASE” density functional method software developed by the “Revolutionary Simulation Software Research and Development” project of the Ministry of Education, Culture, Sports, Science and Technology of Japan.
    The PHASE I/F also supports the “Advance/PHASE V2.5” software developed and sold by AdvanceSoft Corporation.
  • An interface is provided for using the “ADF” density functional method software developed and sold by Scientific Computing & Modelling NV. In SCIGRESS V2, an interface is provided for the “ADF BAND” periodic boundary structure calculation in addition to the existing ADF interface function.
  • An interface is provided for using the “CONFLEX 7” conformation space search software developed and sold by Conflex Corporation.
  • An interface is provided for using the “MOPAC2009” semiempirical molecular orbital software developed and sold by Stewart Computational Chemistry.
  • An interface is provided for using the “GAMESS” nonempirical molecular orbital and density functional software being primarily developed by the Gordon research group of Iowa State University.

 PHASE interface

PHASE interface

Input/Output File Format Conversion

SCIGRESS can import and export file formats used by other applications.

SCIGRESS can import the following file formats:

  • Tribble format
  • Brookhaven format (PDB)
  • MDL Mol format
  • SYBYL Mol format

SCIGRESS can export the following file formats:

  • Brookhaven format (PDB)
  • MDL Mol format
  • Shelx format
  • Cambridge format
  • Crystal Structure format
  • SYBYL Mol format
  • Gaussian fchk format  

Chemical Structure Editor Interoperation Function

  • This function allows chemical structure editors to be used to construct the molecular structures to be calculated.
  • SCIGRESS is able to interoperate with the ChemDraw structure drawing software made by CambridgeSoft, if it is installed.
Chemical Structure EditorChemical Structure Editor

Can be selected to suit the application and purpose of your chemistry or materials research

You can choose from among five packages depending on the applications and goals of your chemistry or materials research. Options can also be added as needed.

Product Lineup

SCIGRESS Basic

This is the basic package that combines the basic modeling tools and calculation engine. This is best for computational chemistry basic educational purposes, people who want to interoperate with their own applications, and people who mainly use a GUI environment that combines interface options.

MO (MO-G & MO-S)

This is a product for performing molecular orbital calculations using the “MO-G” and “MO-S” semiempirical molecular orbital engines.

MD-ME

This is a product for performing molecular dynamics calculations using the “MD-ME” molecular dynamics engine.

Spreadsheet

This is a product for performing batch calculations of various molecular structures using the spreadsheet.

Components

Comosition


Note 1: The MO I/F needs to be purchased in order to use the MO calculation engine.

Note 2: The MD I/F needs to be purchased in order to use the MD calculation engine.

Note 3: The ADF calculation engine itself needs to be purchased separately.

Note 4: The PHASE calculation engine itself needs to be downloaded separately from the developer’s website (free version) or purchased (paid version).

Note 5: The CONFLEX6 calculation engine itself needs to be purchased separately.

Refer to the “Functions” page for details on other options.

License System

The number of machines that can be used simultaneously on the network is up to the number of licenses purchased (network licenses). There is no limit on the number of installations.
You can choose between perpetual or annual licenses.
Please contact us if you want multiple licenses.

Pricing

Please contact us using the contact details below for information on pricing.
Separate educational institution pricing is also available.

(Note)Installation and support costs are quoted separately.

Runs on Windows. Linux options are also available (MD-ME, MO). Parallel processing is available on Linux

Windows

OS CPU Memory HDD
Windows Vista 32-bit / 64-bit edition
Windows 7 32-bit / 64-bit edition
Windows 8 32-bit / 64-bit edition
Pentium 4 
3GHz or higher
(Pentium M 1GHz or higher)
Recommended 2GB or more
(1GB)
Free space of 2GB
(200MB)
Other
[Monitor]
Resolution of 1,024×768 pixels or higher, 32,768 colors or more (800×600 pixels or higher, 256 colors or more)
[Video cards where operation has been verified]
RADEON X300 SE
Intel GMA3100
Intel GMA950
Intel 82865G
On some machines that use the integrated graphics chipsets for Intel CPUs, monochrome display and screen redraw might not operate correctly. People using these systems should notify us in advance. Chipset-related information can be checked using the following method.
XP: Control Panel -> Display -> Advanced Settings in the Settings tab -> Adapter
Vista: Control Panel -> Personalization -> Advanced Settings in Display Settings -> Adapters
OS CPU Memory HDD
RedHat Enterprise Linux 5
RedHat Enterprise Linux 6
CentOS 5
CentOS 6
Pentium 4
3GHz or higher
Recommended 2GB or more
(1GB)
2GB or more free space

(Note) Values in parentheses are minimum requirements. Please consult us for OSs and processors other than as above.