Scalable molecular dynamics with NAMD

By James C. Phillips, Rosemary Braun, Wei Wang, James C. Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant V. Kalé, Klaus Schulten. 2005

16,410 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

Biological and synthetic membranes: What can be learned from a coarse-grained description? (2006, methodology): “Most of the program packages (NAMD, GROMACS, DL POLY, LAMMPS and ESPResSo) are freely available.”
Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS (2015, methodology): “This means that the most suitable parallelization is the offloadmodel, which other MD codes have also employed successfully [9,18].”
General purpose molecular dynamics simulations fully implemented on graphics processing units (2008, methodology): “During the last decade, general purpose MD codes such as LAMMPS [3], DLPOLY [4], GROMACS [5], NAMD [6] and ESPResSO [7] have been developed to run very efficiently on distributed memory computer clusters.”
Identification of an allosteric modulator of the serotonin transporter with novel mechanism of action. (2013, methodology): “Ten structures of SERT were modeled, among which one low-energy structure was subjected to further refinement using energy minimization and constrained MD simulation using NAMD2 (Phillips et al., 2005).”
Molecular dynamics simulations of protein dynamics and their relevance to drug discovery. (2010, methodology): “NAMD is in many ways the opposite of CHARMM in usability; it has a much simpler scripting language and reduced functionally.”
Self-diffusion coefficient of bulk and confined water: a critical review of classical molecular simulation studies (2018, methodology): “Although, this was a great issue in the early days of molecular simulations, nowadays with the huge increase in computational power and the availability of highly parallelizable open-source codes (LAMMPS [9], GROMACS [10], and NAMD [370]), such effects can be mitigated up to a point, especially for ”
Graphene microsheets enter cells through spontaneous membrane penetration at edge asperities and corner sites (2013, methodology): “Phillips JC, et al. (2005) Scalable molecular dynamics with NAMD.”