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.

• Molecular Dynamics

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.

• Steered molecular dynamics (SMD)
• Replica exchange molecular dynamics (REMD)
• Targeted molecular dynamics (TMD)
• Coarse-grained dynamics
• Scalable molecular dynamics
• Interactive molecular dynamics
• Free Energy Calculation

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.

• Relative binding free energy calculation
• Free energy perturbation calculation
• Alchemical free energy perturbation calculation
• Result Analysis

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.

• Cluster analysis
• Electrostatic interaction analysis
• RMSD, RMSF analysis
• PCA analysis service
• Secondary structure analysis

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

• 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.