Molecular Dynamics Applications
MD is a computer simulation of physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a period of time, giving a view of the motion of the atoms. Leverage Nimbix optimized accelerated resources to aid in MD modeling, simulations, and analysis. Don't see your application? Request a new application or read about running your application on our framework.
ACEMDACEMD is a production bio-molecular dynamics (MD) software specially optimized to run on graphics processing units (GPUs) on NVIDIA graphics cards. ACEMD is the world fastest MD engine for a single workstation allowing performance equivalent to over 100 CPUs and microsecond long trajectories. ACEMD reads CHARMM/NAMD and AMBER input files on a simple, yet powerful configuration interface.
AMBERAMBER allows the ability to use NVIDIA GPUs to accelerate PMEMD for both explicit solvent PME and implicit solvent GB simulations.
AbaloneAbalone is a general purpose molecular modeling program focused on molecular dynamics of biopolymers. In addition, it can interact with external quantum chemical programs NWChem, CP2K and PC GAMESS/Firefly).
CHARMMCHARMM 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
DL-POLYDL_POLY is a general purpose classical molecular dynamics (MD) simulation software developed at Daresbury Laboratory by I.T. Todorov and W. Smith.
GROMACSGROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.
HOOMD-BlueHOOMD-blue stands for Highly Optimized Object-oriented Many-particle Dynamics -- Blue Edition. It performs general purpose particle dynamics simulations on a single workstation, taking advantage of NVIDIA GPUs to attain a level of performance equivalent to many processor cores on a fast cluster.
LAMMPSLAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) 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.
NAMDNAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using gigabit ethernet.
OpenMMOpenMM is a library which provides tools for modern molecular modeling simulation. As a library it can be hooked into any code, allowing that code to do molecular modeling with minimal extra coding. Moreover, OpenMM has a strong emphasis on hardware acceleration, thus providing not just a consistent API, but much greater performance than what one could get from just about any other code available.
Bioinformatics deals with the study of methods for storing, retrieving and analyzing biological data, such as nucleic acid (DNA/RNA) and protein sequences, structures, functions, pathways, and genetic interactions.
Computational chemistry uses the results of theoretical chemistry, incorporated into efficient computer programs, to calculate the structures and properties of molecules and solids.
Computational finance applies computer science and emphasizes practical numerical methods rather than mathematical proofs and focuses on techniques that apply directly to economic analyses.
Computational fluid dynamics uses numerical methods and algorithms to perform the calculations required to simulate the interaction of liquids and gases with surfaces defined by boundary conditions.
Computer Aided Engineering (CAE) is the use of computer software to simulate performance in order to improve product designs or assist in the resolution of engineering problems for a wide range of industries. This includes simulation, validation, and optimization of products, processes, and manufacturing tools.
Data mining attempts to extract information from a data set and transform it into an understandable structure for further use.
Molecular docking predicts the preferred orientation of one molecule to a second when bound to each other to form a stable complex in order to understand the strength of association or binding affinity between the two molecules.
Electronic Design Automation (EDA or ECAD) tools aid chip designers in creating electronic systems such as printed circuit boards and integrated circuits.
Geophysics is the study of the Earth using quantitative physical methods. Seismic analysis is the process of transforming seismic reflection data into a quantitative rock-property description of a reservoir. These applications have many uses in oil and gas industries.
Materials science investigates the relationship between the structure of materials at atomic or molecular scales and their macroscopic properties by incorporating elements of applied physics and chemistry.
Physics is a natural science that involves the study of matter and its motion through space and time, along with related concepts such as energy and force.
Rendering generates an image from a model, by means of computer programs for applications such as architecture, video games, simulators, movie or TV visual effects, and design visualization.
Video processing allows information to be gathered from a video or a video be encoded into a different format.
Weather and climate models use quantitative methods to simulate the interactions of the atmosphere, oceans, land surface, and ice.