Audience
Biophysicists, structural biologists, and molecular simulation researchers requiring a biomolecular simulation tool for desktops, clusters, GPUs, and supercomputers
About NAMD
NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, it scales from desktop and laptop computers to high-end parallel platforms, hundreds of cores for typical simulations, and beyond 500,000 cores for the largest simulations. NAMD is built for researchers who need to simulate large molecular systems efficiently while preserving compatibility with widely used molecular modeling workflows. It uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, and it is file-compatible with AMBER, CHARMM, and X-PLOR. It is designed to support biomolecular simulations involving proteins, membranes, nucleic acids, solvents, ions, and other molecular systems where atomic interactions and time-dependent motion need to be studied in detail.
Other Popular Alternatives & Related Software
Ascalaph Designer
Ascalaph Designer is a general-purpose program for molecular dynamic simulations. Under a single graphical environment are represented as their own implementation of molecular dynamics as well as the methods of classical and quantum mechanics of popular programs. Molecular geometry optimization with conjugate gradient methods. Shows molecular models in separate windows. Each window has two cameras, which allow the model to be simultaneously visualized from two sides and in different graphic modes. The subwindow can be opened by dragging the splitter in the right corner of each graphical window. Clicking on an atom or bond with the left mouse button slightly changes their color and a brief info about the picked object appears in the status bar. The wire-frame style is convenient for large molecules, particularly, proteins. Drawing is very fast for this style. Finally, CPK wire frame combines the properties of several above styles.
Learn more
ESPResSo
ESPResSo, the Extensible Simulation Package for Research on Soft Matter, is a highly versatile open source simulation package for performing and analyzing scientific molecular dynamics and Monte Carlo many-particle simulations. It is designed as a universal tool for simulating a variety of soft matter systems, especially coarse-grained atomistic or bead-spring models used in physics, chemistry, molecular biology, and process engineering. ESPResSo can be used to simulate polymers, liquid crystals, colloids, polyelectrolytes, ferrofluids, gels, biological systems, DNA, lipid membranes, bacterial motion, and super-capacitors. In coarse-grained models, a group of atoms or molecules is treated as a single bead, allowing researchers to investigate larger time and length scales than would be practical with fully atomistic simulations. ESPResSo supports classical molecular dynamics simulations in different statistical ensembles.
Learn more
Promethium
Promethium is a GPU-powered chemistry simulation platform designed to accelerate drug and materials development by enabling faster and more accurate quantum chemistry calculations. Built from the ground up for NVIDIA datacenter GPUs like A100, it employs novel QC Ware streaming algorithms to achieve unprecedented computational speed and high throughput-to-power consumption ratios. It supports density functional theory calculations on systems with up to 2,000 atoms, allowing simulations of large molecular systems that are not feasible with legacy CPU-powered ab initio codes. For instance, a single-point calculation of a 2,056-atom protein can be completed in 14 hours on a single GPU. Promethium offers a range of capabilities, including single-point energy calculations, geometry optimization, conformer search, torsion scan, reaction path optimization, transition state optimization, interaction energy computations, and relaxed potential energy surface scans.
Learn more
LAMMPS
LAMMPS, the Large-scale Atomic/Molecular Massively Parallel Simulator, is a classical molecular dynamics code with a focus on materials modeling. It models ensembles of particles in liquid, solid, or gaseous states and can simulate atomic, polymeric, biological, solid-state, granular, coarse-grained, mesoscopic, or macroscopic systems using many interatomic potentials, force fields, and boundary conditions. LAMMPS can model systems in two or three dimensions, from only a few particles up to billions, and is designed to run efficiently on parallel computers while remaining easy to extend and modify. It includes potentials for solid-state materials such as metals and semiconductors, soft matter such as biomolecules and polymers, and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generally, as a parallel particle simulator at atomic, meso, or continuum scale.
Learn more
Pricing
Starting Price:
Free
Free Version:
Free Version available.
Integrations
No integrations listed.
Company Information
Theoretical and Computational Biophysics Group
Founded: 2006
United States
www.ks.uiuc.edu/Research//namd/
Videos and Screen Captures
Other Useful Business Software
One Subscription for Email, Storage, Meetings, and AI
Get a custom business email at your domain, up to 5TB of pooled storage per user, video meetings with recording and noise cancellation, eSignature in Docs, and appointment booking through Calendar. Real-time collaboration across every device, with enterprise-grade security built in.
Product Details
Platforms Supported
Windows
Mac
Linux
Training
Documentation
Support
Online
