No Access Submitted: 19 May 2020 Accepted: 01 July 2020 Published Online: 30 July 2020
J. Chem. Phys. 153, 044130 (2020); https://doi.org/10.1063/5.0014475
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  • James C. Phillips
  • David J. Hardy
  • Julio D. C. Maia
  • John E. Stone
  • João V. Ribeiro
  • Rafael C. Bernardi
  • Ronak Buch
  • Giacomo Fiorin
  • Jérôme Hénin
  • Wei Jiang
  • Ryan McGreevy
  • Marcelo C. R. Melo
  • Brian K. Radak
  • Robert D. Skeel
  • Abhishek Singharoy
  • Yi Wang
  • Benoît Roux
  • Aleksei Aksimentiev
  • Zaida Luthey-Schulten
  • Laxmikant V. Kalé
  • Klaus Schulten
  • Christophe Chipot
  • Emad Tajkhorshid
NAMD is 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.
NAMD core development has been supported by the National Institutes of Health (NIH), Grant No. P41-GM104601 (to E.T., K.S., A.A., L.V.K., and Z.L.-S.). Additional support for specific algorithm/software development was provided by NIH R01-GM072558 (to B.R.), and the National Science Foundation, Grant Nos. PHY-1430124 (to Z.L.-S., K.S., and A.A.), MCB-1616590 (to Z.L.-S. and R.C.B.), MCB-1517221 (to B.R.), and MCB-1942763 (to A.S.), and the Agence Nationale de la Recherche grant ProteaseInAction. NAMD development and testing and simulation of specific molecular systems were enabled by NSF resources provided through multiple XSEDE and PRAC allocations at the National Center for Supercomputing Applications (NCSA) and the Texas Advanced Computing Center (TACC), as well as resources at DOE National Laboratories through leadership allocations (INCITE) and early science and application readiness projects at Oak Ridge National Laboratory (ORNL), Argonne National Laboratory (ANL), and the National Energy Research Scientific Computing Center (NERSC). Significant technical and development assistance for NAMD and Charm++ was contributed by the NCSA, ORNL, and ANL leadership computing centers as well as by the technology companies NVIDIA, IBM, Intel, AMD, Mellanox, and Cray.
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