Cerius²

The leading modeling and simulation environment for SGI IRIX workstations and other servers, Cerius² provides a wealth of tools for applications ranging from material science modeling to life science modeling and simulations.

Cerius² provides an easy-to-use simulation and modeling environment, offering a broad range of scientific application modules. Different Cerius2 modules are available, allowing you to adapt your research for creating a customized and integrated package.

System Requirements
C² requires a Silicon Graphics workstation running IRIX 6.5.10 or higher. This release includes external LigandFit executables for three platforms: SGI/IRIX, LINUX and IBM/AIX. The hosts supported for external parallel LigandFit are SGI machines running IRIX 6.5.10 through 6.5.19, Linux machines running RedHat 6.2, 7.1 or 7.2, and IBM machines running AIX version 5.1.0.0. For SGI machines running IRIX 6.5.1 to 6.5.9, the users may obtain a patch from SGI to run LigandFit.

C²·Open Force Field
C²·Open Force Field is an environment designed to maximize the effectiveness, flexibility, and ease-of-use of forcefield-based atomistic simulation methods. Atomistic simulation assists research in areas including catalysis, separations, crystallization, polymer sciences, drug discovery, and protein engineering. It explains relationships between structure and molecular behavior, provides insight into key molecular interactions, and predicts critical properties of solids, liquids, and gases. A fundamental requirement for such simulation is a means of evaluating and analyzing the energy of the molecular system. Forcefields do this rapidly and with sufficient accuracy to support many valuable computations.

Forcefields approximate energy by summing a series of empirical terms representing the steric, chemical, and electrostatic interactions in a molecular system. The functional forms and parameters that make up these energy terms are validated using experimental data or accurate quantum mechanics calculations. A forcefield is dependent upon the molecular system used in this parameterization - generally, it works well for molecules or materials that are chemically similar to this system. A wide range of forcefields is thus required to accurately describe the diverse systems studied using atomistic simulation.

C²·Open Force Field lets you choose, edit, and apply the forcefields that you need to solve your research problems.

What C²·Open Force Field Does For You
C²·Open Force Field gives you straightforward access to valuable forcefield technology. These forcefields are used by Cerius2 calculations to compute energies, analyze different energetic contributions, and evaluate energy gradients as molecular systems change. You select any one of an extensive library of forcefields by clicking on its name within the Cerius2 user interface. Sensible default parameters are chosen for your system during the automatic set-up procedure. Then you simply run your calculation.

C²·Open Force Field draws together, in a single environment, the results of many years of scientific research, including some of the best validated forcefields currently available. These parameterizations come from the scientific literature and respected simulation packages such as Discover. They support calculations on biological compounds (1), polymers (2), organic molecules (3), homogeneous catalysts (4), zeolites (5), glasses (6), and many other systems. Accelrys' documentation, on-line help, and customer support helps you to choose and apply the correct forcefield.

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SGI Power Station

Our SGI Octane2 workstation w/ IRIX 6.5.22 is fully dedicated to running Cerius². The Silicon Graphics Octane2 visual workstation delivers the world's most advanced desktop visualization. Octane2 combines the ground-breaking VPro 3D graphics system, the industry-leading crossbar architecture, and the latest high-performance MIPS® processor in an affordable power desktop package.

Octane2 delivers a suite of industry-leading options including the award-winning DMediaProTM DM2 video option for the most powerful high-definition solution on the desktop. Complementing DM2 is the new DMediaPro DM5 for high-quality uncompressed HD and SD graphics-to-video output from 3D graphics, 2D imagery, and video data. Other innovative options include the Dual Head and Dual Channel Display options, which maximize your visualization resources, and the new cost-effective PowerDuo configuration, which allows two users to share the same high-performance system.

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Gaussian 03 and GaussView 03

Gaussian 03 is the latest in the Gaussian series of electronic structure programs. Gaussian 03 is used by chemists, chemical engineers, biochemists, physicists and others for research in established and emerging areas of chemical interest.

Starting from the basic laws of quantum mechanics, Gaussian predicts the energies, molecular structures, and vibrational frequencies of molecular systems, along with numerous molecular properties derived from these basic computation types. It can be used to study molecules and reactions under a wide range of conditions, including both stable species and compounds which are difficult or impossible to observe experimentally such as short-lived intermediates and transition structures.

Gaussian 03 expands the range of chemical systems that it can model to periodic systems such as polymers and crystals via its periodic boundary conditions (PBC) methods. The PBC technique models these systems as repeating unit cells in order to determine the structure and bulk properties of the compound.

For example, Gaussian 03 can predict the equilibrium geometries and transition structures of polymers. It can also study polymer reactivity by predicting isomerization energies, reaction energetics, and so on, allowing the decomposition, degradation, and combustion of materials to be studied. Gaussian 03 can also model compounds’ band gaps.

Other PBC capabilities in Gaussian 03:

• 2D PBC methods can be used to model surface chemistry, such as reactions on surfaces and catalysis. In addition, using Gaussian 03 allows you to study the same problem using a surface model and/or a cluster model, using the same basis set and Hartree-Fock or DFT theoretical method in both cases. Using Gaussian 03 enables you to choose the appropriate approach for the system you are studying, rather than being forced to frame the problem to fit the capabilities and limitations of a particular model.

• 3D PBC: The structures and available bulk properties of crystals and other three-dimensional periodic systems can be predicted

Predicting Spectra
Gaussian 03 can compute a very wide range of spectra and spectroscopic properties. These include:

• IR and Raman
• Pre-resonance Raman
• UV-Visible
• NMR
• Vibrational circular dichroism (VCD)
• Electronic circular dichroism (ECD)
• Optical rotary dispersion (ORD)
• Harmonic vibration-rotation coupling
• Anharmonic vibration and vibration-rotation coupling
• g tensors and other hyperfine spectra tensors

For example, Gaussian 03 computes many of the tensors which contribute to hyperfine spectra. These results are useful for making spectral assignments for observed peaks, something which is usually difficult to determine solely from the experimental data. Using theoretical predictions to aid in interpreting and fitting observed results should make non-linear molecules as amenable to study as linear ones.

Modeling Solvent Effects on Reactions and Molecular Properties
Molecular properties and chemical reactions often vary considerably between the gas phase and in solution. For example, low lying conformations can have quite different energies in the gas phase and in solution (and in different solvents), conformation equilibria can differ, and reactions can take significantly different paths. Gaussian 03 offers the Polarizable Continuum Model (PCM) for modeling system in solution. This approach represents the solvent as a polarizable continuum and places the solute in a cavity within the solvent.

GaussView 3.0

GaussView 3.0 makes using Gaussian 03 simple and straightforward:

Sketch in molecules using its advanced 3D Structure Builder, or load in molecules from standard files.
Set up and submit Gaussian 03 jobs right from the interface, and monitor their progress as they run.
Examine calculation results graphically via state-of-the-art visualization features: display molecular orbitals and other surfaces, view spectra, animate normal modes, geometry optimizations and reaction paths.
GaussView supports all Gaussian 03 features, and it includes graphical facilities for generating keywords and options, molecule specifications and other input sections for even the most advanced calculation types. GaussView makes it simple to set up ONIOM layers, unit cells for Periodic Boundary Conditions jobs, CASSCF active spaces, molecule specifications for transition structure optimizations using the STQN method, and so on.

Building Molecules
GaussView includes an advanced Molecule Builder. You can use it to rapidly sketch in molecules and examine them in three dimensions. You can build molecules by atom, ring, group, amino acid and nucleoside, and you can also open PDB and other standard molecule files (hydrogen atoms can be added automatically with excellent accuracy and reliability).

Setting Up Gaussian 03 Calculations
GaussView’s Gaussian Calculation Setup window allows you to set up Gaussian 03 jobs in a simple and straightforward manner. All of the features of Gaussian 03 are supported by the interface, enabling you to prepare input for any job type.

Visualizing Gaussian Results
GaussView can graphically display a variety of Gaussian calculation results, including the following:

• Molecular orbitals

• Atomic charges

• Surfaces from the electron density, electrostatic potential, NMR shielding density, and other properties. Surfaces may be displayed in solid, translucent and wire mesh modes.

• Surfaces can be colored by a separate property.

• Animation of the normal modes corresponding to vibrational frequencies.

• Animation of the steps in geometry optimizations, potential energy surface scans, intrinsic reaction coordinate (IRC) paths, and molecular dynamics trajectories from BOMD and ADMP calculations.

Animating Optimizations and Reaction Paths

GaussView 3.0 introduces several new animation capabilities in addition to displaying molecular vibrations corresponding to normal modes present in earlier versions. These new animation sequences can be viewed with GaussView, and the individual frames can be saved for import into animation/movie editing software.

Setting Up Jobs for Periodic Systems
Gaussian 03 can perform Periodic Boundary Conditions (PBC) calculations in order to model periodic systems in condensed phases such as polymers, surfaces and crystals. GaussView 3.0 provides a rich PBC facility for creating the molecule specifications for such calculations, and the program takes care of creating the appropriate Gaussian 03 input from your graphically defined unit cell.

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