Cepos InSilico. EMPIRE™.Semiempirical molecular orbital program designed to run in parallel on multi-core desktop computers and on massively parallel supercomputers.

EMPIRE™ and EH5cube™

EMPIRE™

EMPIRE™ is a modern, parallel (but not linear scaling) semiempirical molecular orbital program that can treat extremely large systems (it has been tested up to 100,000 atoms for non-periodic calculations and for repeat units in periodic calculations up to 50,000 atoms). EMPIRE™ scales well up to thousands of cores, depending on the size of the system. There is no software-imposed upper limit to the size of the systems that can be calculated.
EMPIRE is particularly interesting for materials science because it can calculate extensive crystalline systems with defects or dopants, amorphous systems (by using very large repeat units), 2D electronic devices and self-organized aggregates. Because it does not use any local approximations, EMPIRE™ is particularly suitable for electroactive systems.
In biology and medicinal chemistry, EMPIRE™ serves as the compute engine for quantum-mechanical-based computer-aided drug design or to investigate the properties of entire proteins, for instance for electron-transfer in redox-active proteins.
For simulations of soft matter, EMPIRE™ is often used to perform single-point calculations on snapshots taken from classical molecular-dynamics simulations within an ensemble model.
EMPIRE™ currently offers the MNDO, MNDO/D, AM1, PM3, PM6, RM1, hpCADD and MNDO-F Hamiltonians. All EMPIRE™ parameter files are in an easily readable ASCII format and include all necessary information to characterize the Hamiltonian completely. EMPIRE™ calculations are thus completely transparent and custom Hamiltonians can be implemented easily by the user.

Dispersion-bound Plastic Crystals: MNDO-F molecular dynamics

EMPIRE™ not only includes a very efficient and effective Born-Oppenheiner molecular-dynamics capability [1] but also the novel MNDO-F Hamiltonian, which includes dispersion interactions in MNDO using an innovative “Feynman” perturbation of the electron density. [2-4]
The following video shows the results of an MNDO-F non-periodic NVT molecular-dynamics simulation of a cluster of 36 adamantane molecules (936 atoms) in the gas phase at 298 K. This cluster is bound only by dispersion forces but does not dissociate with the 75 ps simulation, demonstrating the excellent description of dispersion in MNDO-F:

Video: Adamantane Cluster (298 K)

A longer (1 ns) NVT simulation at 298 K demonstrates the evaporation of the cluster. This ten-minute video shows the first 0.4 ns of the trajectory:

Video: Evaporation of the Adamantane Cluster (298 K)

At room temperature, adamantane exists as a plastic crystalline phase, which means that the molecules can rotate on their crystal lattice sites. [5] The following video shows the central adamantane molecule in a 75 picosecond 3D-periodic NVT simulation of the adamantane crystal at 400K with MNDO-F (36 adamantane molecules in the repeat unit). The rotation of the central molecule on its lattice site can be seen near the end of the simulation.

Video: Adamantane Crystal (400 K)

Fullerene collision and fusion to a C₁₂₀ fullertube

The following video shows the results of an MNDO-F UHF singlet (broken symmetry) simulation of the collision of two C₆₀ fullerenes that initially approach each other at a combined speed of 600 m s^-1. The trajectory consists of 5 ps NVE simulation (black background) followed by 10 ps NVT simulation at 1000K (gray background, animation speed doubled) and 10 ps NVT at 298K (silver background). The collision results in the formation of a distorted C₁₂₀ fullertube that would eventually anneal to a conventional fullertube structure.

Video: Fullerene collision and fusion to a C120 fullertube (1000 and 298 K)

Program versions

EMPIRE20™ has now been released. It includes the following new features:

Self-consistent reaction field implicit solvent simulations for ground states. These calculations allow fast convergence for proteins, which now no longer need explicit water molecules.
Transition-state optimizations using the NS01A algorithm.
Localized molecular orbitals.
Atomic multipole analysis.
Excited states for open-shell molecules with an improved UNO-CI formalism.
The initial guess can now be read from and EMPIRE _e.h5 HDF5 output file.

EMPIRE19™ includes both extensions of the functionality and performance enhancements compared to its predecessor (EMPIRE14™):

Improved performance: Among other performance enhancements, the calculation of gradients has been speeded up significantly. This improvement speeds up geometry optimizations and numerical calculations of the normal vibrations, especially for periodic systems, where the improvement is largest.
Normal vibrations: EMPIRE19™ can now calculate normal vibrations (frequencies and eigenvectors) using a finite-difference numerical approach.
New Hamiltonians: The following new Hamiltonians have been implemented

PM6 – Stewart’s most popular Hamiltonian
RM1 – an improved parameterization of AM1
hpCADD – a dedicated Hamiltonian for calculating properties such as the molecular electrostatic potential. hpCADD is only suitable for single-point calculations
MNDO-F – MNDO extended with the new self-consistent, multi-center, anisotropic “Feynman” dispersion correction

Free academic version of EMPIRE™

Annual single-seat licenses for the single-node version of EMPIRE™ are freely available for bona fide academic users. To register and download the program, please click here.

EH5cube™

EH5cube™ is the postprocessor for EMPIRE™ calculations. EMPIRE™ writes a small ASCII output file that contains only the most important information. Its primary (and most detailed) output is a binary wavefunction file in the platform-independent HDF5 format. It is possible to recreate essentially all electronic properties of the molecule or periodic system from the information contained in the .h5 file. EH5cube™ reads the .h5 file and creates, for instance, Gaussian cube files containing the electron density, molecular orbitals or local properties (local ionization energy, local electron affinity or local polarization), either on a grid or at points in space specified in the program input.

CADDLE.^®

A customizable and entirely web-based molecular modeling system including single-node EMPIRE20™ ...more (visit the product side)

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