Applications of Nanoscale Molecular Dynamics Software

Applications of Nanoscale Molecular Dynamics Software

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.

Our Services Based on NAMD Designer Software

On the NAMD software platform, CD ComputaBio can provide customers with high-quality computational biology services.

Our Capabilities

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.

The Features of NAMD Software

Applications of Nanoscale Molecular Dynamics Software

  • Support Alchemical free energy perturbation free energy calculation.
  • Support Adaptive biasing force potential of mean force calculation.
  • Support CHARMM, Amber, GROMACS force field, and can directly read the parameter files of these three software. Among them, CHARMM force field can be fully supported, and Amber and GROMACS can do most of them.
  • Supports an implicit solvent model based on the Generalized Born model, similar to Amber
  • The force field function form provided by NAMD can support the OPLS force field, but the user must convert the OPLS parameter file format first.
  • Multiple steered molecular dynamics methods are supported.
* For Research Use Only.