High-performance scalable molecular dynamics simulations of a polarizable force field based on classical Drude oscillators in NAMD
W Jiang, DJ Hardy, JC Phillips… - The journal of …, 2011 - ACS Publications
Incorporating the influence of induced polarization in large-scale atomistic molecular
dynamics (MD) simulations is a critical challenge in the progress toward computations of …
dynamics (MD) simulations is a critical challenge in the progress toward computations of …
Molecular dynamics simulations using the drude polarizable force field on GPUs with OpenMM: Implementation, validation, and benchmarks
Presented is the implementation of the Drude force field in the open‐source OpenMM
simulation package allowing for access to graphical processing unit (GPU) hardware. In the …
simulation package allowing for access to graphical processing unit (GPU) hardware. In the …
Implementation of extended L agrangian dynamics in GROMACS for polarizable simulations using the classical D rude oscillator model
Explicit treatment of electronic polarization in empirical force fields used for molecular
dynamics simulations represents an important advancement in simulation methodology. A …
dynamics simulations represents an important advancement in simulation methodology. A …
An empirical polarizable force field based on the classical drude oscillator model: development history and recent applications
Molecular mechanics force fields that explicitly account for induced polarization represent
the next generation of physical models for molecular dynamics simulations. Several …
the next generation of physical models for molecular dynamics simulations. Several …
Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields
We present Tinker-HP, a massively MPI parallel package dedicated to classical molecular
dynamics (MD) and to multiscale simulations, using advanced polarizable force fields (PFF) …
dynamics (MD) and to multiscale simulations, using advanced polarizable force fields (PFF) …
Tinker-HP: Accelerating molecular dynamics simulations of large complex systems with advanced point dipole polarizable force fields using GPUs and multi-GPU …
O Adjoua, L Lagardère, LH Jolly… - Journal of chemical …, 2021 - ACS Publications
We present the extension of the Tinker-HP package (Lagardère, Chem. Sci. 2018, 9, 956−
972) to the use of Graphics Processing Unit (GPU) cards to accelerate molecular dynamics …
972) to the use of Graphics Processing Unit (GPU) cards to accelerate molecular dynamics …
Towards exact molecular dynamics simulations with machine-learned force fields
Molecular dynamics (MD) simulations employing classical force fields constitute the
cornerstone of contemporary atomistic modeling in chemistry, biology, and materials …
cornerstone of contemporary atomistic modeling in chemistry, biology, and materials …
Polarizable force field for DNA based on the classical Drude oscillator: I. Refinement using quantum mechanical base stacking and conformational energetics
JA Lemkul, AD MacKerell Jr - Journal of chemical theory and …, 2017 - ACS Publications
Empirical force fields seek to relate the configuration of a set of atoms to its energy, thus
yielding the forces governing its dynamics, using classical physics rather than more …
yielding the forces governing its dynamics, using classical physics rather than more …
[HTML][HTML] Scalable molecular dynamics on CPU and GPU architectures with NAMD
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 …
large biological objects on CPU-and GPU-based architectures. NAMD offers scalable …
Efficient particle-mesh Ewald based approach to fixed and induced dipolar interactions
We have implemented classical Ewald and particle-mesh Ewald (PME) based treatments of
fixed and induced point dipoles into the sander molecular dynamics (MD) module of AMBER …
fixed and induced point dipoles into the sander molecular dynamics (MD) module of AMBER …