Nanoscale Molecular Dynamics (NAMD) is computer software for molecular dynamics simulations written using the Charm++ parallel programming model. It is known for its parallel efficiency and is often used to simulate large systems (millions of atoms). It was developed in collaboration between the Theoretical and Computational Biophysics Group (TCB) and the Parallel Programming Laboratory (PPL) at the University of Illinois at Urbana-Champaign. The developers of NAMD have positioned the software's most important feature as scalability, specifically targeting massively high-performance parallel computing. It is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on the Charm++ parallel object, NAMD scales to hundreds of cores for typical simulations and to over 500,000 cores for maximum simulations. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also compatible with AMBER, CHARMM and X-PLOR files.
On the NAMD software platform, CD ComputaBio can provide customers with high-quality computational biology services.
Before using NAMD for molecular dynamics simulation, we need to prepare various necessary data files for NAMD to be used by NAMD. Our scientists will prepare PDB file, PSF file, force field file, and configuration file for your simulation systems.
One of the most important tasks in drug design is to predict which drugs will bind more strongly to a therapeutic target in a set of lead drug candidates. CD ComputaBio provides every new drug developer with binding free energy calculations to provide design ideas that accelerate development and save costs.
Our scientists can analyze the NAMD simulation results in conjunction with VMD. As a complementary software co-developed with NAMD, VMD fully matches NAMD in terms of file format and interactive interface, and the two can be seamlessly connected.
On the NAMD software platform, our scientists can provide our customers with molecular simulation, building crystal, structure optimization, geometry optimization and chemical force field development.