Studies of excited electronic states and other “multireference” problems are possible using the equation-of-motion (EOM) coupled-cluster techniques. These techniques which are closely related to (and in some cases identical to) so-called Fock space multireference coupled-cluster theory, offer a powerful means to study open-shell systems and decided advantages when configuration mixing is important. At present, these include the EOMEE approach for singlet and triplet excited states, and the EOMIP and EOMEA methods that are best applied to low-spin doublet states. Analytic derivatives are available for these methods.

A number of methodological developments have been added to the program in the last two decades. These include: analytic second derivatives for all coupled-cluster approaches up to full CCSDT, the calculation of NMR chemical shifts at MP and CC levels of theory, the calculation of anharmonic force fields (via numerical differentation of analytic derivatives), relativistic corrections, corrections to the Born-Oppenheimer approximation at the CC level, nonadiabatic coupling within the EOM framework, and several others.

-is a versatile and widely used molecular simulation program with broad application to many-particle systems

-has been developed with a primary focus on the study of molecules of biological interest, including peptides, proteins, prosthetic groups, small molecule ligands, nucleic acids, lipids, and carbohydrates, as they occur in solution, crystals, and membrane environments

-provides a large suite of computational tools that encompass numerous conformational and path sampling methods, free energy estimates, molecular minimization, dynamics, and analysis techniques,and model-building capabilities

-is useful for a much broader class of many-particle systems

-can be utilized with various energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potentials with explicit solvent and various boundary conditions, to implicit solvent and membrane models

-has been ported to numerous platforms in both serial and parallel architectures

• Simulation: Perform calculations using Molecular Mechanics (MM), Molecular Dynamics (MD), Quantum Mechanics (QM) and hybrid QM/MM

• Macromolecule Design and and Analysis: Undertake sequence alignments and analysis, 3D structure prediction (MODELER) and validation, structure ionization, predict protein-protein docking (ZDOCK), and even undertake protein engineering and optimization of biophysical properties, including thermal stability and prediction of protein aggregation.

• Small Molecule Design: Using a broad portfolio of scientific technologies, calculate ligand properties and ligand efficiency, perform ligand profiling and filtering using well understood characteristics of drugs, including permeability and undesirable feature metrics, and select optimal subsets using either molecular diversity or cluster-based methods. In addition, it includes specialist tools for:

– Pharmacophore Modeling: Specialist tools for small molecule screening and profiling. Includes tools for both pharmacophore generation, validation and virtual screening, as well as ligand profiling.

– Receptor-ligand Interactions: Undertake Structure-Based Design (SBD), including both fast and physics-based ligand docking (also with flexible docking tools for both ligand and receptor side-chains), combinatorial chemistry library design and optimization tools, fragment-based drug-design (FBDD) tools and de novo ligand design.

• QsAR and ADMET: Create and validate statistical models against biologically important end-points. Alternatively, make use of our pre-built validated models for a broad range of critical pharmacological end- points, including: aqueous solubility, Blood-Brain Barrier penetration, intestinal absorption, Hepatotoxicity and many more.

Firefly has been constantly being developed to incorporate new functionality, improve performance, and extend existing features. For example, Firefly uses real time data compression/decompression, efficient modern algorithms of 2-e integral evaluation for direct calculation methods, very efficient MP2 energy and energy gradient modules, very fast RHF MP3/MP4 energy code, and state-of-the-art DFT, TDDFT, MCSCF, MRMP2, MCQDPT, and XMCQDPT implementation. Firefly runs parallel on SMP systems, clusters of computers, or both; with special attention paid to good scalability even on large clusters and many-core systems.

GaussView is a graphical user interface designed to be used with Gaussian to make calculations easier, quicker and more efficient.

You define particle initial conditions and interactions in a high-level python script. Then tell HOOMD-blue how you want to execute the job and it takes care of the rest. Python job scripts give you unlimited flexibility to create custom initialization routines, control simulation parameters, and perform in situ analysis.

LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale.

LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality.

MDAnalysis allows one to read molecular dynamics trajectories and access the atomic coordinates through NumPy arrays. This provides a flexible and relatively fast framework for complex analysis tasks. In addition, powerful atom selection commands are implemented. Trajectories can also be manipulated (for instance, fit to a reference structure) and written out.

NWChem software can handle
• Biomolecules, nanostructures, and solid-state
• From quantum to classical, and all combinations
• Ground and excited-states
• Gaussian basis functions or plane-waves
• Scaling from one to thousands of processors
• Properties and relativistic effects

XCrySDen has been also ported to MAC OSX (requires X11) and Windows (requires CYGWIN).

The name of the program stands for Crystalline Structures and Densities and X because it runs under the X-Window environment.

Yambo is an important member of the key group of ab initio spectroscopy codes supported by the European Theoretical Spectroscopy Facility.