Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald.

By Romelia Salomón-Ferrer, Andreas W. Götz, Duncan Poole, S. Le Grand, Ross C. Walker. Journal of Chemical Theory and Computation, 2013

3,077 citations recorded by the source corpus.

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

Markov state models of biomolecular conformational dynamics (2014, background): “While computational advances have ushered in a new era of molecular simulation software accelerated by graphics processing hardware [40–42] or even custom ASICs [2], raw advances in computational power are insufficient to produce more than anecdotal observations of protein folding or unfolding event”
GPU-accelerated molecular dynamics and free energy methods in Amber18: performance enhancements and new features (2018, methodology): “In order to address this issue in AMBER, new precision models 6,31 have been developed that leverage ﬁ xed-point integer arithmetic to replace slow double-precision arithmetic in certain key steps when higher precision is required, such as the accumulation of components of the force.”
Accelerating Drugs Discovery with Deep Reinforcement Learning: An Early Approach (2018, methodology): “Applications such as BUDE [34], AMBER [43], BINDSURF [44] or METADOCK [18] use GPUs to overcome this problem by dividing the whole protein surface into independent regions or spots.”