Pre‐exascale HPC approaches for molecular dynamics simulations. Covid‐19 research: A use case
Exascale computing has been a dream for ages and is close to becoming a reality that will
impact how molecular simulations are being performed, as well as the quantity and quality of …
impact how molecular simulations are being performed, as well as the quantity and quality of …
[HTML][HTML] Multiscale biomolecular simulations in the exascale era
The complexity of biological systems and processes, spanning molecular to macroscopic
scales, necessitates the use of multiscale simulations to get a comprehensive …
scales, necessitates the use of multiscale simulations to get a comprehensive …
All-Atom Biomolecular Simulation in the Exascale Era
Exascale supercomputers have opened the door to dynamic simulations, facilitated by AI/ML
techniques, that model biomolecular motions over unprecedented length and time scales …
techniques, that model biomolecular motions over unprecedented length and time scales …
[PDF][PDF] Co-design for molecular dynamics: An exascale proxy application
J Mohd-Yusof, S Swaminarayan, TC Germann - LA-UR 13-20839, 2013 - lanl.gov
Roadrunner demonstrated the need to understand the interaction between high-
performance hardware and software as early in the development process as possible. One …
performance hardware and software as early in the development process as possible. One …
AceCloud: molecular dynamics simulations in the cloud
MJ Harvey, G De Fabritiis - 2015 - ACS Publications
We present AceCloud, an on-demand service for molecular dynamics simulations.
AceCloud is designed to facilitate the secure execution of large ensembles of simulations on …
AceCloud is designed to facilitate the secure execution of large ensembles of simulations on …
Constant-pH molecular dynamics simulations for large biomolecular systems
An increasingly important endeavor is to develop computational strategies that enable
molecular dynamics (MD) simulations of biomolecular systems with spontaneous changes in …
molecular dynamics (MD) simulations of biomolecular systems with spontaneous changes in …
Fostering discoveries in the era of exascale computing: How the next generation of supercomputers empowers computational and experimental biophysics alike
MCR Melo, RC Bernardi - Biophysical Journal, 2023 - cell.com
Over a century ago, physicists started broadly relying on theoretical models to guide new
experiments. Soon thereafter, chemists began doing the same. Now, biological research …
experiments. Soon thereafter, chemists began doing the same. Now, biological research …
Accelerating COVID-19 drug discovery with high-performance computing
A Heifetz - High Performance Computing for Drug Discovery and …, 2023 - Springer
The recent COVID-19 pandemic has served as a timely reminder that the existing drug
discovery is a laborious, expensive, and slow process. Never has there been such global …
discovery is a laborious, expensive, and slow process. Never has there been such global …
Making it rain: cloud-based molecular simulations for everyone
We present a user-friendly front-end for running molecular dynamics (MD) simulations using
the OpenMM toolkit on the Google Colab framework. Our goals are (1) to highlight the usage …
the OpenMM toolkit on the Google Colab framework. Our goals are (1) to highlight the usage …
[图书][B] Understanding molecular simulation: from algorithms to applications
Understanding Molecular Simulation explains molecular simulation from a chemical-physics
and statistical-mechanics perspective. It highlights how physical concepts are used to …
and statistical-mechanics perspective. It highlights how physical concepts are used to …