Scalable molecular dynamics on CPU and GPU architectures with NAMD.

By James C. Phillips, David J. Hardy, Julio D C Maia, John E. Stone, João V. Ribeiro, R. Bernardi, Ronak Buch, G. Fiorin, J'erome H'enin, Wei Jiang and 13 more. Journal of Chemical Physics, 2020

2,675 citations recorded by the source corpus.

NAMDis a molecular dynamics program designed for high-performance simulations of very large biological objects on CPU- and GPU-based architectures. NAMD offers scalable performance on petascale parallel supercomputers consisting of hundreds of thousands of cores, as well as on inexpensive commodity clusters commonly found in academic environments. It is written in C++ and leans on Charm++ parallel objects for optimal performance on low-latency architectures. NAMD is a versatile, multipurpose code that gathers state-of-the-art algorithms to carry out simulations in apt thermodynamic ensembles, using the widely popular CHARMM, AMBER, OPLS, and GROMOS biomolecular force fields. Here, we review the main features of NAMD that allow both equilibrium and enhanced-sampling molecular dynamics simulations with numerical efficiency. We describe the underlying concepts utilized by NAMD and their implementation, most notably for handling long-range electrostatics; controlling the temperature, pressure, and pH; applying external potentials on tailored grids; leveraging massively parallel resources in multiple-copy simulations; and hybrid quantum-mechanical/molecular-mechanical descriptions. We detail the variety of options offered by NAMD for enhanced-sampling simulations aimed at determining free-energy differences of either alchemical or geometrical transformations and outline their applicability to specific problems. Last, we discuss the roadmap for the development of NAMD and our current efforts toward achieving optimal performance on GPU-based architectures, for pushing back the limitations that have prevented biologically realistic billion-atom objects to be fruitfully simulated, and for making large-scale simulations less expensive and easier to set up, run, and analyze. NAMD is distributed free of charge with its source code at www.ks.uiuc.edu.

Subfields: Biomedical Engineering, Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/235b82169c6bfab170e24f31f85854264e4a07b7

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Citations in the corpus

Integrating model simulation tools and cryo‐electron microscopy (2022, background): “246 Due to the complexity and expertise required to build robust visualization software, many of the most popular tools have convergently evolved to support plugins and extension mechanisms, allowing their powerful graphical capabilities to be adapted to new tasks.”
Enhanced Sampling Methods for Molecular Dynamics Simulations [Article v1.0] (2022, methodology): “The Colvars Module is interfaced with NAMD [236], LAMMPS [237], GROMACS [238], and VMD [239] for colvar analysis [240].”
Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development (2020, methodology): “A larger number of software packages for MD of biomolecules are available, for example, GROMACS [9], AMBER [10], NAMD [11], and CHARMM [12]. equation of motion, F = ma (where F is the force exerted on the particle, m is its mass, and a is its acceleration under a potential field), such that the part”