ACEMD is a production molecular dynamics software specially optimized to run on NVIDIA graphics processing units (GPUs). ACEMD is the world’s fastest molecular dynamics engine for a single workstation and can read the popular CHARMM and AMBER force field formats without any change.
AMBER is a suite of molecular modeling and molecular dynamics simulation tools, available for both CPUs and GPUs. AMBER refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules that are in the public domain, and are used in a variety of simulation programs; and a package of molecular simulation programs.
Charmm is a versatile and widely used molecular simulation program with broad application to many-particle systems. Charmm has been developed with a primary focus on the study of molecules of biological interest, such as peptides, proteins, prosthetic groups, small molecule ligands, nucleic acids, lipids, and carbohydrates, as they occur in solution, crystals, and membrane environments. Charmm 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. Charm can also be useful for a much broader class of many-particle systems and 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.
ESPResSo is a highly versatile software package for performing and analyzing scientific Molecular Dynamics many-particle simulations of coarse-grained atomistic or bead-spring models as they are used in soft-matter research in physics, chemistry and molecular biology. It can be used to simulate systems such as polymers, liquid crystals, colloids, ferrofluids and biological systems, for example DNA and lipid membranes.
GPUGRID is a distributed computing infrastructure devoted to biomedical research. GPUGRID scientists can perform molecular simulations to understand the function of proteins in health and disease.
GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics package primarily designed for simulation of proteins, lipids, and nucleic acids. GROMACS is one of the fastest and most popular molecular dynamics software packages available, and can run on CPUs as well as GPUs.
LAMMPS (Large-scale Atomic/Molecular Massivley Parallel Simulator) is an open-source molecular dynamics simulator written in C++ from Sandia National Laboratories, and is designed for parallel machines. LAMMPS models an ensemble of particles in a liquid, solid or gaseous state. It can model atomic polymeric, biological, metallic, or mesoscale systems using a variety of force fields and boundary conditions and is easily extensible.
NAMD 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 cores for typical simulations and beyond 200,000 cores for the largest simulations. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM and X-PLOR. NAMD is distributed free of charge with source code. You can build NAMD yourself or download binaries for a wide variety of platforms.
OpenMM is a toolkit for molecular simulation. It can be used either as a stand-alone application for running simulations, or as a library you call from your own code. It provides a combination of extreme flexibility (through custom forces and integrators), openness, and high performance (especially on recent GPUs) that make it truly unique among simulation codes.
RELION, for REgularized LIkelihood OptimizatioN, is an open-source computer program for the refinement of macromolecular structures by single-particle analysis of electron cryo-microscopy (cryo-EM) data. Whereas alternative approaches often rely on user expertise for the tuning of parameters, RELION uses a Bayesian approach to infer parameters of a statistical model from the data.
CryoSPARC™ is an easy to use software tool that enables rapid, unbiased structure discovery of proteins and molecular complexes from cryo-EM data.
SPHIRE is a new software suite designed for easy access to cryo electron microscopy with the clear goal of quality assessment and result reproducibility by statistical resampling. While being well suited for cryo-EM novices, experienced users will find comfort in the accessibility of almost every possible variable in advanced option tabs and the transparent, easily customizable Python-based framework for non-standard processing pipelines. In a visually appealing and easy-to-use graphical user interface (GUI) the user will find an array of programs which will guide through the complete process of high-resolution cryo-EM.
PHENIX is a software suite for the automated determination of molecular structures using X-ray crystallography and other methods.
VASP is a complex package for performing ab-initio quantum-mechanical molecular dynamics (MD) simulations using pseudopotentials or the projector-augmented wave method and a plane wave basis set. The approach implemented in VASP is based on the (finite-temperature) local-density approximation with the free energy as variational quantity and an exact evaluation of the instantaneous electronic ground state at each MD time step. VASP uses efficient matrix diagonalization schemes and an efficient Pulay/Broyden charge density mixing. These techniques avoid all problems possibly occurring in the original Car-Parrinello method, which is based on the simultaneous integration of electronic and ionic equations of motion. The interaction between ions and electrons is described by ultra-soft Vanderbilt pseudopotentials (US-PP) or by the projector-augmented wave (PAW) method. US-PP (and the PAW method) allow for a considerable reduction of the number of plane-waves per atom for transition metals and first row elements. Forces and the full stress tensor can be calculated with VASP and used to relax atoms into their instantaneous ground-state.
VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS-X, Unix, or Windows, is distributed free of charge, and includes source code.
Bitplane's core scientific module, IMARIS, delivers all the necessary functionality for data visualization, analysis, segmentation and interpretation of 3D and 4D microscopy datasets.
A high-performance Molecular Dynamics code, together with continuously advancing computer hardware technologies, can be used to perform simulations on time scales that illuminate these important biological processes. Desmond, created by D. E. Shaw Research, provides an unprecedented combination of parallel scalability, simulation throughput, and scientific accuracy to achieve these goals.
Integrated solution for atomic-scale simulation of chemical systems
The Rosetta software suite includes algorithms for computational modeling and analysis of protein structures. It has enabled notable scientific advances in computational biology, including de novo protein design, enzyme design, ligand docking, and structure prediction of biological macromolecules and macromolecular complexes.
Slurm is a highly configurable open source workload and resource manager. In its simplest configuration, Slurm can be installed and configured in a few minutes. Use of optional plugins provides the functionality needed to satisfy the needs of demanding HPC centers with diverse job types, policies and work flows. Advanced configurations use plug-ins to provide features like accounting, resource limit management, by user or bank account, and support for sophisticated scheduling algorithms.